Compositions and methods for the treatment and diagnosis of cardiovascular disease using rchd534 as a target

ABSTRACT

The present invention relates to methods and compositions for the treatment and diagnosis of cardiovascular disease, including, but not limited to, atherosclerosis, ischemia/reperfusion, hypertension, restenosis, and arterial inflammation. Specifically, the present invention identifies and describes genes which are differentially expressed in cardiovascular disease states, relative to their expression in normal, or non-cardiovascular disease states, and/or in response to manipulations relevant to cardiovascular disease. Further, the present invention identifies and describes genes via the ability of their gene products to interact with gene products involved in cardiovascular disease. Still further, the present invention provides methods for the identification and therapeutic use of compounds as treatments of cardiovascular disease. Moreover, the present invention provides methods for the diagnostic monitoring of patients undergoing clinical evaluation for the treatment of cardiovascular disease, and for monitoring the efficacy of compounds in clinical trials. Additionally, the present invention describes methods for the diagnostic evaluation and prognosis of various cardiovascular diseases, and for the identification of subjects exhibiting a predisposition to such conditions.

This is a division of application Ser. No. 08/485,573, filed Jun. 7,1995, now U.S. Pat. No. 5,968,770 which in turn is acontinuation-in-part of application Ser. No. 08/386,844, filed Feb. 10,1995, each of which is hereby incorporated by reference in its entirety.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY-SPONSOREDRESEARCH AND DEVELOPMENT

Part of the work performed during development of this invention utilizedU.S. Government funds. The U.S. Government has certain rights in thisinvention. This work was supported by National Institutes of HealthGrants P50-HL56985 and R37-HL-51150.

1. INTRODUCTION

The present invention relates to methods and compositions for thetreatment and diagnosis of cardiovascular disease, including, but notlimited to, atherosclerosis, ischemia/reperfusion, hypertension,restenosis, and arterial inflammation. Genes which are differentiallyexpressed in cardiovascular disease states, relative to their expressionin normal, or non-cardiovascular disease states are identified. Genesare also identified via the ability of their gene products to interactwith other gene products involved in cardiovascular disease. The genesidentified may be used diagnostically or as targets for therapeuticintervention. In this regard, the present invention provides methods forthe identification and therapeutic use of compounds in the treatment anddiagnosis of cardiovascular disease. Additionally, methods are providedfor the diagnostic monitoring of patients undergoing clinical evaluationfor the treatment of cardiovascular disease, for monitoring the efficacyof compounds in clinical trials, and for identifying subjects who may bepredisposed to cardiovascular disease.

2. BACKGROUND OF THE INVENTION

Cardiovascular disease is a major health risk throughout theindustrialized world. Atherosclerosis, the most prevalent ofcardiovascular diseases, is the principal cause of heart attack, stroke,and gangrene of the extremities, and thereby the principle cause ofdeath in the United States. Atherosclerosis is a complex diseaseinvolving many cell types and molecular factors (for a detailed review,see Ross, 1993, Nature 362: 801-809). The process, in normalcircumstances a protective response to insults to the endothelium andsmooth muscle cells (SMCs) of the wall of the artery, consists of theformation of fibrofatty and fibrous lesions or plaques, preceded andaccompanied by inflammation. The advanced lesions of atherosclerosis mayocclude the artery concerned, and result from an excessiveinflammatory-fibroproliferative response to numerous different forms ofinsult. For example, shear stresses are thought to be responsible forthe frequent occurrence of atherosclerotic plaques in regions of thecirculatory system where turbulent blood flow occurs, such as branchpoints and irregular structures.

The first observable event in the formation of an atherosclerotic plaqueoccurs when blood-borne monocytes adhere to the vascular endotheliallayer and transmigrate through to the sub-endothelial space. Adjacentendothelial cells at the same time produce oxidized low densitylipoprotein (LDL). These oxidized LDL's are then taken up in largeamounts by the monocytes through scavenger receptors expressed on theirsurfaces. In contrast to the regulated pathway by which native LDL(nLDL) is taken up by nLDL specific receptors, the scavenger pathway ofuptake is not regulated by the monocytes.

These lipid-filled monocytes are called foam cells, and are the majorconstituent of the fatty streak. Interactions between foam cells and theendothelial and SMCs which surround them lead to a state of chroniclocal inflammation which can eventually lead to smooth muscle cellproliferation and migration, and the formation of a fibrous plaque. Suchplaques occlude the blood vessel concerned and thus restrict the flow ofblood, resulting in ischemia.

Ischemia is a condition characterized by a lack of oxygen supply intissues of organs due to inadequate perfusion. Such inadequate perfusioncan have number of natural causes, including atherosclerotic orrestenotic lesions, anemia, or stroke, to name a few. Many medicalinterventions, such as the interruption of the flow of blood duringbypass surgery, for example, also lead to ischemia. In addition tosometimes being caused by diseased cardiovascular tissue, ischemia maysometimes affect cardiovascular tissue, such as in ischemic heartdisease. Ischemia may occur in any organ, however, that is suffering alack of oxygen supply.

The most common cause of ischemia in the heart is atheroscleroticdisease of epicardial coronary arteries. By reducing the lumen of thesevessels, atherosclerosis causes an absolute decrease in myocardialperfusion in the basal state or limits appropriate increases inperfusion when the demand for flow is augmented. Coronary blood flow canalso be limited by arterial thrombi, spasm, and, rarely, coronaryemboli, as well as by ostial narrowing due to luetic aortitis.Congenital abnormalities, such as anomalous origin of the left anteriordescending coronary artery from the pulmonary artery, may causemyocardial ischemia and infarction in infancy, but this cause is veryrare in adults. Myocardial ischemia can also occur if myocardial oxygendemands are abnormally increased, as in severe ventricular hypertrophydue to hypertension or aortic stenosis. The latter can be present withangina that is indistinguishable from that caused by coronaryatherosclerosis. A reduction in the oxygen-carrying capacity of theblood, as in extremely severe anemia or in the presence ofcarboxy-hemoglobin, is a rare cause of myocardial ischemia. Notinfrequently, two or more causes of ischemia will coexist, such as anincrease in oxygen demand due to left ventricular hypertrophy and areduction in oxygen supply secondary to coronary atherosclerosis.

The principal surgical approaches to the treatment of ischemicatherosclerosis are bypass grafting, endarterectomy, and percutaneoustranslumenal angioplasty (PCTA). The failure rate after these approachesdue to restenosis, in which the occlusions recur and often become evenworse, is extraordinarily high (30-50%). It appears that much of therestenosis is due to further inflammation, smooth muscle accumulation,and thrombosis.

Very recently, a modified balloon angioplasty approach was used to treatarterial restenosis in pigs by gene therapy (Ohno et al., 1994, Science265: 781-784). A specialized catheter was used to introduce arecombinant adenovirus carrying the gene encoding thymidine kinase (tk)into the cells at the site of arterial blockage. Subsequently, the pigswere treated with ganciclovir, a nucleoside analog which is converted bytk into a toxic form which kills cells when incorporated into DNA.Treated animals had a 50% to 90% reduction in arterial wall thickeningwithout any observed local or systemic toxicities.

Because of the presumed role of the excessiveinflammatory-fibroproliferative response in atherosclerosis andischemia, a number of researchers have investigated, in the context ofarterial injury, the expression of certain factors involved ininflammation, cell recruitment and proliferation. These factors includegrowth factors, cytokines, and other chemicals, including lipidsinvolved in cell recruitment and migration, cell proliferation and thecontrol of lipid and protein synthesis.

For example, the expression of PDGF (platelet derived growth factor) orits receptor was studied: in rats during repair of arterial injury(Majesky et al., 1990, J. Cell Biol. 111: 2149); in adherent cultures ofhuman monocyte-derived macrophages treated with oxidized LDL (Malden etal., 1991, J. Biol. Chem. 266: 13901); and in bovine aortic endothelialcells subjected to fluid shear stress (Resnick et al., 1993, Proc. Natl.Acad. Sci. USA 90: 4591-4595). Expression of IGF-I (insulin-like growthfactor-I) was studied after balloon deendothelialization of rat aorta(Cercek et al., 1990, Circulation Research 66: 1755-1760).

Other studies have focused on the expression of adhesion-molecules onthe surface of activated endothelial cells which mediate monocyteadhesion. These adhesion molecules include intracellular adhesionmolecule-1, ICAM-1 (Simmons et al., 1988, Nature, 331: 624-627), ELAM(Bevilacqua et al., 1989, Science 243: 1160-1165; Bevilacqua et al.,1991, Cell 67: 233), and vascular cell adhesion molecule, VCAM-1 (Osbornet al., 1989, Cell 59: 1203-1211); all of these surface molecules areinduced transcriptionally in the presence of IL-1. Histological studiesreveal that ICAM-1, ELAM and VCAM-1 are expressed on endothelial cellsin areas of lesion formation in vivo (Cybulsky et al., 1991, Science251: 788-791; 1991, Arterioscler. Thromb. 11: 1397a; Poston et al.,1992, Am. J. Pathol. 140: 665-673). VCAM-1 and ICAM-1 were shown to beinduced in cultured rabbit arterial endothelium, as well as in culturedhuman iliac artery endothelial cells by lysophophatidylcholine, a majorphospholipid component of atherogenic lipoproteins. (Kume et al., 1992,J. Clin. Invest. 90: 1138-1144). VCAM-I, ICAM-1, and class II majorhistocompatibility antigens were reported to be induced in response toinjury to rabbit aorta (Tanaka, et al., 1993, Circulation 88:1788-1803).

Recently, cytomegalovirus (CMV) has been implicated in restenosis aswell as atherosclerosis in general (Speir, et al., 1994, Science 265:391-394). It was observed that the CMV protein IE84 apparentlypredisposes smooth muscle cells to increased growth at the site ofrestenosis by combining with and inactivating p53 protein, which isknown to suppress tumors in its active form.

The foregoing studies are aimed at defining the role of particular geneproducts presumed to be involved in the excessiveinflammatory-fibroproliferative response leading to atheroscleroticplaque formation. However, such approaches cannot identify the fullpanoply of gene products that are involved in the disease process, muchless identifying those which may serve as therapeutic targets for thediagnosis and treatment of various forms of cardiovascular disease.

3. SUMMARY OF THE INVENTION

The present invention relates to methods and compositions for thetreatment and diagnosis of cardiovascular disease, including but notlimited to, atherosclerosis, ischemia/reperfusion, hypertension,restenosis, and arterial inflammation. Specifically, genes areidentified and described which are differentially expressed incardiovascular disease states, relative to their expression in normal,or non-cardiovascular disease states.

“Differential expression”, as used herein, refers to both quantitativeas well as qualitative differences in the genes' temporal and/or tissueexpression patterns. Differentially expressed genes may represent“fingerprint genes,” and/or “target genes.” “Fingerprint gene,” as usedherein, refers to a differentially expressed gene whose expressionpattern may be utilized as part of a prognostic or diagnosticcardiovascular disease evaluation, or which, alternatively, may be usedin methods for identifying compounds useful for the treatment ofcardiovascular disease. “Target gene”, as used herein, refers to adifferentially expressed gene involved in cardiovascular disease suchthat modulation of the level of target gene expression or of target geneproduct activity may act to ameliorate a cardiovascular diseasecondition. Compounds that modulate target gene expression or activity ofthe target gene product can be used in the treatment of cardiovasculardisease.

Further, “pathway genes” are defined via the ability of their productsto interact with other gene products involved in cardiovascular disease.Pathway genes may also exhibit target gene and/or fingerprint genecharacteristics. Although the genes described herein may bedifferentially expressed with respect to cardiovascular disease, and/ortheir products may interact with gene products important tocardiovascular disease, the genes may also be involved in mechanismsimportant to additional cardiovascular processes.

The invention includes the products of such fingerprint, target, andpathway genes, as well as antibodies to such gene products. Furthermore,the engineering and use of cell- and animal-based models ofcardiovascular disease to which such gene products may contribute arealso described.

The present invention encompasses methods for prognostic and diagnosticevaluation of cardiovascular disease conditions, and for theidentification of subjects exhibiting a predisposition to suchconditions. Furthermore, the invention provides methods for evaluatingthe efficacy of drugs, and monitoring the progress of patients, involvedin clinical trials for the treatment of cardiovascular disease.

The invention also provides methods for the identification of compoundsthat modulate the expression of genes or the activity of gene productsinvolved in cardiovascular disease, as well as methods for the treatmentof cardiovascular disease which may involve the administration of suchcompounds to individuals exhibiting cardiovascular disease symptoms ortendencies.

The invention is based, in part, on systematic search strategiesinvolving in vivo and in vitro cardiovascular disease paradigms coupledwith sensitive and high throughput gene expression assays. In contrastto approaches that merely evaluate the expression of a given geneproduct presumed to play a role in a disease process, the searchstrategies and assays used herein permit the identification of allgenes, whether known or novel, that are expressed or repressed in thedisease condition, as well as the evaluation of their temporalregulation and function during disease progression. This comprehensiveapproach and evaluation permits the discovery of novel genes and geneproducts, as well as the identification of an array of genes and geneproducts (whether novel or known) involved in novel pathways that play amajor role in the disease pathology. Thus, the invention allows one todefine targets useful for diagnosis, monitoring, rational drug screeningand design, and/or other therapeutic intervention.

In the working examples described herein, eight novel human genes areidentified that are demonstrated to be differentially expressed indifferent cardiovascular disease states. Additionally, the differentialexpression of three previously identified human genes is described. Theidentification of these genes and the characterization of theirexpression in particular disease states provide newly identified rolesin cardiovascular disease for both the novel genes and the known genes.

Bcl-2 and glutathione peroxidase are the products of known genes thatare shown herein to be down regulated in monocytes of patients exposedto an atherogenic high fat/high cholesterol diet. Furthermore,counteracting the down-regulation of bcl-2 under atherogenic conditions,as described herein, may ameliorate atherosclerosis. Accordingly,methods are provided for the diagnosis, monitoring in clinical trials,and treatment of cardiovascular disease based upon the discoveriesherein regarding the expression patterns of bcl-2 and glutathioneperoxidase. Because these two genes were known to be involved inpreventing apoptosis, the discovery of their down-regulation underatherogenic conditions provides a novel, positive correlation betweenapoptosis and atherogenesis. Accordingly, methods provided herein fordiagnosing, monitoring, and treating cardiovascular disease may also bebased on a number of genes involved in the apoptotic pathway, includingbut not limited to ICE (IL-1 converting enzyme); Bad; BAG-1 (Bcl-2associated athanogene 1, Takayama et al., 1995, Cell 80: 279-284); BAX(Bcl-2 associated X protein, Oltvai et al., 1993, Cell 74: 609-619);BClX_(L) (Boise, et al., 1993, Cell 74: 597-608); BAK (Bcl-2 antagonistkiller, Farrow et al., 1995. Nature 374: 631-733); and Bcl-X_(s)(Tsujmoto et al., 1984, Science 226: 1097-1099) . The cardiovasculardiseases that may be so diagnosed, monitored in clinical trials, andtreated include but are not limited to atherosclerosis,ischemia/reperfusion, and restenosis.

rchd005, rchd024, rchd032, and rchd036 are newly identified genes thatare each up-regulated in endothelial cells treated with IL-1.Accordingly, methods are provided for the diagnosis, monitoring inclinical trials, and treatment of cardiovascular disease based upon thediscoveries herein regarding the expression patterns of rchd005,rchd024, rchd032, and rchd036.

Endoperoxide synthase is a known gene, and rchd502, rchd523, rchd528,and rchd534 are newly identified genes that are each up-regulated inendothelial cells subjected to shear stress. Accordingly, methods areprovided for the diagnosis, monitoring in clinical trials, screening fortherapeutically effective compounds, and treatment of cardiovasculardisease based upon the discoveries herein regarding the expressionpatterns of endoperoxide synthase, rchd502, rchd523, rchd528, andrchd534.

More specifically, because each of these genes is up-regulated either byIL-1 (rchd005, rchd024, rchd032, and rchd036) or by shear stress(endoperoxide synthase, rchd502, rchd523, rchd528, and rchd534),treatment methods can be designed to reduce or eliminate theirexpression, particularly in endothelial cells. Alternatively, treatmentmethods include inhibiting the activity of the protein products of thesegenes. In addition, detecting expression of these genes in excess ofnormal expression provides for the diagnosis of cardiovascular disease.Furthermore, in testing the efficacy of compounds during clinicaltrials, a decrease in the level of the expression of these genescorresponds to a return from a disease condition to a normal state, andthereby indicates a positive effect of the compound. The cardiovasculardiseases that may be so diagnosed, monitored in clinical trials, andtreated include but are not limited to atherosclerosis,ischemia/reperfusion, hypertension, restenosis, and arterialinflammation.

The rchd523 gene can be a particularly useful target for treatmentmethods as well as diagnostic and clinical monitoring methods. As atransmembrane protein, the rchd523 gene product is accessible from thecell surface. Accordingly, natural ligands, derivatives of naturalligands, and antibodies that bind to the rchd523 gene product can beutilized to inhibit its activity, or alternatively, to target thespecific destruction of cells that are in the disease state.Furthermore, the extracellular domains of the rchd523 gene productprovide especially efficient screening systems for identifying compoundsthat bind to the rchd523 gene product. Compounds that bind the receptordomain of the rchd523 gene product, for example, can be identified bytheir ability to mobilize Ca²⁺ and thereby produce a fluorescent signal,as described in Section 5.5.1, below.

Such an assay system can also be used to screen and identify antagonistsof the interaction between the rchd523 gene product and ligands thatbind to the rchd523 gene product. For example, the compounds can competewith the endogenous (i.e., natural) ligand for the rchd523 gene product.The resulting reduction in the amount of ligand-bound rchd523 genetransmembrane protein will modulate the activity of disease state cells,such as endothelial cells. Soluble proteins or peptides, such aspeptides comprising one or more of the extracellular domains, orportions and/or analogs thereof of the rchd523 gene product, including,for example, soluble fusion proteins such as Ig-tailed fusion proteins,can be particularly useful for this purpose.

Similarly, antibodies that are specific to one or more of theextracellular domain of the rchd523 product provide for the readydetection of this target gene product in diagnostic tests or in clinicaltest monitoring. Accordingly, endothelial cells can be treated, eitherin vivo or in vitro, with such a labeled antibody to determine thedisease state of endothelial cells. Because the rchd523 gene product isup-regulated in endothelial cells under shear stress, its detectionpositively corresponds with cardiovascular disease.

The examples presented in Sections 6-9, below, demonstrate the use ofthe cardiovascular disease paradigms of the invention to identifycardiovascular disease target genes.

The example presented in Section 10, below, demonstrates the use offingerprint genes in diagnostics and as surrogate markers for testingthe efficacy of candidate drugs in basic research and in clinicaltrials.

The example presented in Section 11, below, demonstrates the use offingerprint genes, particularly rchd523, in the imaging of a diseasedcardiovascular tissue.

The example presented in Section 12, below, demonstrates the use oftarget genes, particularly rchd523, in screening for ligands of targetgene product receptor domains, as well as antagonists of theligand-receptor interaction.

4. DESCRIPTION OF THE FIGURES

FIG. 1. In vivo cholesterol differential display. mRNA prepared fromhuman monocytes isolated from the blood of patients on different diets.cDNA prepared from one patient on a high fat diet/high serum cholesterol(lanes 1,2) and low fat diet/low serum cholesterol (lanes 3,4) wasdisplayed using the forward primer T₁₁XG (SEQ ID NO:8) and the reverseprimer OP014 (agcatggctc; SEQ ID NO:9). The DNA corresponding to markedband (#14) was excised and amplified for sequence analysis.

FIG. 2. Band #14 Northern blot analysis. A random primer-labeled band#14 probe was hybridized with a Northern blot prepared from the samepatient's monocytes used in differential display. An 8 kb band was seenin the low fat/low cholesterol conditions, and not in the high fat/highcholesterol conditions.

FIG. 3. Quantitative RT-PCR analysis of mouse bcl-2 mRNA levels inapoE-deficient mice. Monocyte RNA from apoE-deficient and control micewas compared using primers for mouse bcl-2 (for-cacccctggcatcttctccttcc(SEQ ID NO:10)/rev-atcctcccccagttcaccccatcc (SEQ ID NO:11) shown in theupper panel and mouse γActin (for-cctgatagatgggcactgtgt (SEQ IDNO:12)/rev-gaacacggcattgtcactaact (SEQ ID NO:13) shown in the lowerpanel. A 1:3 dilution series of each input cDNA was done in pairs withthe left band in each pair deriving from wild-type cDNA and the rightband from apoE-deficient cDNA.

FIG. 4. RT-PCR quantification of human glutathione peroxidase (HUMGPXP1)cDNA from human clinical samples cDNA prepared from RNA derived fromblood monocytes of the same patient under a high fat diet (serumcholesterol level=200; top panel) and a low fat diet (serum cholesterollevel=170; bottom panel). Dilution series of amplification productsusing GPX1.3 primers derived from HUMGPXP1 sequences 1121-1142(for-aagtcgcgcccgcccctgaaat; SEQ ID NO:14) and 1260-1237(rev-gatccctggccaccgtccgtctga; SEQ ID NO:15) is shown in the leftportion of each panel. Dilution series of amplification products usinghuman actin primers (for accctgaagtaccccat; SEQ IDNO:16/rev-tagaagcatttgcggtg; SEQ ID NO:17) is shown in the right portionof each panel. The HUMGPXP1 band decreased in intensity under a high fatdiet (compare top left to bottom left), whereas the actin control bandwas equally intense under each diet (compare top right to bottom right).

FIG. 5. IL-1 activated HUVEC differential display. mRNA prepared fromcontrol HUVEC (lanes 9,10), 1 hr. of 10 units/ml IL-1 treatment (lanes7,8), or 6 hr. treatment (lanes 11,12), was used in differential displayreactions with the forward primer OPE7 (agatgcagcc; SEQ ID NO:18) andreverse primer T₁₁XA (SEQ ID NO:19), which is an equimolar mix ofoligonucleotides where X is G, C, or A. The DNA corresponding to markedband, rchd005, was excised and amplified for Northern analysis andsubcloning.

FIG. 6. Northern blot analysis of endothelial IL-1 inducible rchd005. 2μg of total RNA from control, 1 hr. and 6 hr. samples was eluted on anagarose gel, blotted, and incubated with a ³²p labeled probe preparedfrom amplified rchd005 sequences. The indicated band migrated withmarkers corresponding to approximately 7.5 kb.

FIG. 7. A Northern blot prepared from shear stressed RNA and hybridizedwith the same rchd005 probe detects a 7.5 kb band up-regulated moststrongly at 1 hr.

FIG. 8. Band rchd005 DNA sequence; SEQ ID NO:1. The sequence wasdetermined by sequencing the insert of pRCHD005, resulting from theligation of amplified rchd005 sequences into the TA cloning vector.

FIG. 9. IL-1 activated HUVEC differential display. mRNA prepared fromcontrol HUVEC (lanes 3,4), 1 hr. of 10 units/ml IL-1 treatment (lanes1,2), or 6 hr. treatment (lanes 5,6), was used in differential displayreactions with the forward primer OPG20 (tctccctcag; SEQ ID NO:20) andreverse primer T₁₁XC (SEQ ID NO:21), which is an equimolar mix ofoligonucleotides where X is G, C, or A. The DNA corresponding to markedband, rchd024, was excised and amplified for Northern analysis andsubcloning.

FIG. 10. Northern blot analysis of endothelial IL-1 inducible bandrchd024. 2 μg of total RNA from control, 1 hr. and 6 hr. samples waseluted on an agarose gel, blotted, and incubated with a ³²p labeledprobe prepared from amplified band rchd024 sequences. The indicated bandmigrated with markers corresponding to approximately 10 kb.

FIG. 11. Shear stress Northern blot analysis of endothelial IL-1inducible band rchd024. A Northern blot prepared from shear stressed RNAand hybridized with the same rchd024 probe detected a 10 kb bandup-regulated most strongly at 6 hr.

FIG. 12. Band rchd024 DNA sequence; SEQ ID NO:2. The sequence wasdetermined by sequencing the insert of pRCHD024, resulting from theligation of amplified rchd024 sequences into the TA cloning vector.

FIG. 13. IL-1 activated HUVEC differential display for rchd032. mRNAprepared from control HUVEC (lanes 3,4), 1 hr. of 10 units/ml IL-1treatment (lanes 1,2) , or 6 hr. treatment (lanes 5,6), was used indifferential display reactions with the forward primer OPI9 (tggagagcag;SEQ ID NO:22) and reverse primer T₁₁XA, which is an equimolar mix ofoligonucleotides where X is G, C, or A. The DNA corresponding to markedband, rchd032, was excised and amplified for Northern analysis andsubcloning.

FIG. 14. RT-PCR quantification of rchd032 cDNA from IL-1 activatedHUVEC's cDNA prepared from RNA derived from control, 1 hr., and 6 hr.IL-1 activated HUVEC's. Shown in lanes 1,2, and 3 are a 5 fold dilutionseries of input cDNA amplified in the upper panel with rchd032 primers(for-atttataaaggggtaattcatta; SEQ ID NO:23/rev-ttaaagccaatttcaaaataat;SEQ ID NO:24), and in the lower panel with human actin primers(for-accctgaagtaccccat/rev-tagaagcatttgcggtg). A band at the 1:125dilution in lane 3 is visible in the 6 hr. sample but not in thecontrol.

FIG. 15. Band rchd032 DNA sequence; SEQ ID NO:3. The sequence wasdetermined by sequencing the insert of pRCHD032, resulting from theligation of amplified rchd032 sequences into the TA cloning vector.

FIG. 16. IL-1 activated HUVEC differential display for rchd036. mRNAprepared from control HUVEC (lanes 3,4), 1 hr. of 10 units/ml IL-1treatment (lanes 1,2), or 6 hr. treatment (lanes 5,6), was used indifferential display reactions with the forward primer OPI17(ggtggtgatg; SEQ ID NO:25) and reverse primer T₁₁XC, which is anequimolar mix of oligonucleotides where X is G, C, or A. The DNAcorresponding to marked band, rchd036, was excised and amplified forNorthern analysis and subcloning.

FIG. 17. Northern blot analysis of endothelial IL-1 inducible bandrchd036. 2 μg of total RNA from control (lane 1), 1 hr. (lane 2), and 6hr. (lane 3) samples was eluted on an agarose gel, blotted, andincubated with a ³²p labeled probe prepared from amplified band rchd036sequences. The indicated band migrated with markers corresponding toapproximately 8 kb.

FIG. 18. Band rchd036 DNA sequence (SEQ ID NO:4). The sequence wasdetermined by sequencing the insert of pRCHD036, resulting from theligation of amplified rchd036 sequences into the TA cloning vector.

FIG. 19. Laminar shear stress HUVEC differential display. mRNA preparedfrom control HUVEC (lanes 3,4), 1 hr. (lanes 1,2) of 10 dyn/cm2 laminarshear stress treatment or 6 hr. treatment (lanes 5,6), was used indifferential display reactions with the forward primer OPE7 (agatgcagcc)and reverse primer T₁₁XA, which is an equimolar mix of oligonucleotideswhere X is G, C, or A. The DNA corresponding to marked band, rchd502,was excised and amplified for Northern analysis and subcloning.

FIG. 20. Northern blot analysis of shear stress inducible band rchd502.2 μg of total RNA from control, 1 hr. and 6 hr. shear stressed sampleswas eluted on an agarose gel, blotted, and incubated with a ³²p labeledprobe prepared from amplified band rchd502 sequences. The indicated bandmigrates with markers corresponding to approximately 4.5 kb.

FIG. 21. Northern blot analysis of shear stress inducible band rchd502on IL-1 blot. 2 μg of total RNA from control (lane 1), 1 hr. (lane 2),and 6 hr. (lane 3) IL-1 induced HUVEC samples was eluted on an agarosegel, blotted, and incubated with a ³²p labeled probe prepared fromamplified band rchd502 sequences. A 4.5 kb band is seen which was notup-regulated by IL-1.

FIGS. 22A-D. Band rchd502 DNA sequence (SEQ ID NO:5). The sequence wasdetermined by sequencing the insert of pRCHD502, resulting from theligation of amplified rchd502 sequences into the TA cloning vector.

FIG. 23. Laminar shear stress HUVEC differential display for rchd505.mRNA prepared from control HUVEC (lanes 3,4), 1 hr. (lanes 1,2) or 6 hr.(lanes 5,6) of 10 dyn/cm2 laminar shear stress treatment was used indifferential display reactions with the forward primer OPE2 (ggtgcgggaa;SEQ ID NO:26) and reverse primer T₁₁XA, which is an equimolar mix ofoligonucleotides where X is G, C, or A. The DNA corresponding to markedband, rchd505, was excised and amplified for Northern analysis andsubcloning.

FIG. 24. Northern blot analysis of shear stress inducible band rchd505.2 μg of total RNA from control, 1 hr. and 6 hr. shear stressed sampleswas eluted on an agarose gel, blotted, and incubated with a ³²p labeledprobe prepared from amplified band rchd505 sequences. The indicated bandmigrated with markers corresponding to approximately 5.0 kb.

FIG. 25. Northern blot analysis of shear stress inducible band rchd505on IL-1 blot. 2μg of total RNA from control (lane 1), 1 hr. (lane 2),and 6 hr. (lane 3) IL-1 induced HUVEC samples was eluted on an agarosegel, blotted, and incubated with a ³²p labeled probe prepared fromamplified band rchd505 sequences. A 5.0 kb inducible band is seen.

FIG. 26. Laminar shear stress HUVEC differential display for rchd523.mRNA prepared from control HUVEC (lanes 3,4), 1 hr. (lanes 1,2) or 6 hr.(lanes 5,6) of 10 dyn/cm2 laminar shear stress treatment was used indifferential display reactions with the forward primer OPI11(acatgccgtg; SEQ ID NO:27) and reverse primer T₁₁XC, which is anequimolar mix of oligonucleotides where X is G,C, or A. The DNAcorresponding to marked band, rchd523, was excised and amplified forNorthern analysis and subcloning.

FIGS. 27A-D. DNA (SEQ ID NO:6) and encoded amino acid (SEQ ID NO:30)sequence of the rchd523 gene.

FIG. 28. Laminar shear stress HUVEC differential display for rchd528.mRNA prepared from control HUVEC (lanes 3,4), 1 hr. (lanes 1,2) or 6 hr.(lanes 5,6) of 10 dyn/cm2 laminar shear stress treatment was used indifferential display reactions with the forward primer OPI19(aatgcgggag; SEQ ID NO:30) and reverse primer T₁₁XG, which is anequimolar mix of oligonucleotides where X is G,C, or A. The DNAcorresponding to marked band, rchd528, was excised and amplified forNorthern analysis and subcloning.

FIG. 29. Northern blot analysis of shear stress inducible band rchd528.2 μg of total RNA from control (lane 1), 1 hr. (lane 2), and 6 hr. (lane3) shear stressed samples was eluted on an agarose gel, blotted, andincubated with a ³²p labeled probe prepared from amplified band rchd528sequences. The indicated band migrated with markers corresponding toapproximately 5.0 kb.

FIGS. 30A-K. Band rchd528 DNA sequence (SEQ ID NO:7). The sequence wasdetermined by sequencing the insert of pRCHD528, resulting from theligation of amplified rchd528 sequences into the TA cloning vector.

FIG. 31. Restriction map of plasmid pScR-bcl2.

FIG. 32. Northern blot analysis of expression of rchd036 mRNA undershear stress. RNA was prepared from HUVEC's that were untreated(control) and treated with shear stress for 1 hr. and 6 hr. The blot wasprobed with labeled rchd036 DNA.

FIG. 33. Northern blot analysis of expression of rchd534 mRNA undershear stress. RNA was prepared from HUVEC's that were untreated(control) and treated with shear stress for 1 hr. and 6 hr. The blot wasprobed with labeled rchd534 DNA.

FIGS. 34A-D. (SEQ ID NO:37). DNA and encoded amino acid (SEQ ID NO:37)sequence of the rchd534 gene.

5. DETAILED DESCRIPTION OF THE INVENTION

Methods and compositions for the diagnosis and treatment ofcardiovascular disease, including but not limited to atherosclerosis,ischemia/reperfusion, hypertension, restenosis, and arterialinflammation, are described. The invention is based, in part, on theevaluation of the expression and role of all genes that aredifferentially expressed in paradigms that are physiologically relevantto the disease condition. This permits the definition of diseasepathways and the identification of targets in the pathway that areuseful both diagnostically and therapeutically.

Genes, termed “target genes” and/or “fingerprint genes” which aredifferentially expressed in cardiovascular disease conditions, relativeto their expression in normal, or non-cardiovascular disease conditions,are described in Section 5.4. Additionally, genes, termed “pathwaygenes” whose gene products exhibit an ability to interact with geneproducts involved in cardiovascular disease are also described inSection 5.4. Pathway genes may additionally have fingerprint and/ortarget gene characteristics. Methods for the identification of suchfingerprint, target; and pathway genes are described in Sections 5.1,5.2, and 5.3.

Further, the gene products of such fingerprint, target, and pathwaygenes are described in Section 5.4.2, antibodies to such gene productsare described in Section 5.4.3, as are cell- and animal-based models ofcardiovascular disease to which such gene products may contribute, inSection 5.4.4.

Methods for the identification of compounds which modulate theexpression of genes or the activity of gene products involved incardiovascular disease are described in Section 5.5. Methods formonitoring the efficacy of compounds during clinical trials aredescribed in Section 5.5.4. Additionally described below, in Section5.6, are methods for the treatment of cardiovascular disease.

Also discussed below, in Section 5.8, are methods for prognostic anddiagnostic evaluation of cardiovascular disease, including theidentification of subjects exhibiting a predisposition to this disease,and the imaging of cardiovascular disease conditions.

5.1. IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES

This section describes methods for the identification of genes which areinvolved in cardiovascular disease, including but not limited toatherosclerosis, ischemia/reperfusion, hypertension, restenosis, andarterial inflammation. Such genes may represent genes which aredifferentially expressed in cardiovascular disease conditions relativeto their expression in normal, or non-cardiovascular disease conditions.Such differentially expressed genes may represent “target” and/or“fingerprint” genes. Methods for the identification of suchdifferentially expressed genes are described, below, in this section.Methods for the further characterization of such differentiallyexpressed genes, and for their identification as target and/orfingerprint genes, are presented, below, in Section 5.3.

“Differential expression” as used herein refers to both quantitative aswell as qualitative differences in the genes' temporal and/or tissueexpression patterns. Thus, a differentially expressed gene may have itsexpression activated or completely inactivated in normal versuscardiovascular disease conditions (e.g., treated with oxidized LDLversus untreated), or under control versus experimental conditions. Sucha qualitatively regulated gene will exhibit an expression pattern withina given tissue or cell type which is detectable in either control orcardiovascular disease subjects, but is not detectable in both.Alternatively, such a qualitatively regulated gene will exhibit anexpression pattern within a given tissue or cell type which isdetectable in either control or experimental subjects, but is notdetectable in both. “Detectable”, as used herein, refers to an RNAexpression pattern which is detectable via the standard techniques ofdifferential display, reverse transcriptase− (RT−) PCR and/or Northernanalyses, which are well known to those of skill in the art.

Alternatively, a differentially expressed gene may have its expressionmodulated, i.e., quantitatively increased or decreased, in normal versuscardiovascular disease states, or under control versus experimentalconditions. The degree to which expression differs in normal versuscardiovascular disease or control versus experimental states need onlybe large enough to be visualized via standard characterizationtechniques, such as, for example, the differential display techniquedescribed below. Other such standard characterization techniques bywhich expression differences may be visualized include but are notlimited to quantitative RT-PCR and Northern analyses.

Differentially expressed genes may be further described as target genesand/or fingerprint genes. “Fingerprint gene,” as used herein, refers toa differentially expressed gene whose expression pattern may be utilizedas part of a prognostic or diagnostic cardiovascular disease evaluation,or which, alternatively, may be used in methods for identifyingcompounds useful for the treatment of cardiovascular disease. Afingerprint gene may also have the characteristics of a target gene.

“Target gene”, as used herein, refers to a differentially expressed geneinvolved in cardiovascular disease in a manner by which modulation ofthe level of target gene expression or of target gene product activitymay act to ameliorate symptoms of cardiovascular disease. A target genemay also have the characteristics of a fingerprint gene.

A variety of methods may be utilized for the identification of geneswhich are involved in cardiovascular disease. These methods include butare not limited to the experimental paradigms described, below, inSection 5.1.1. Material from the paradigms may be characterized for thepresence of differentially expressed gene sequences as discussed, below,in Section 5.1.2.

5.1.1. PARADIGMS FOR THE IDENTIFICATION OF DIFFERENTIALLY EXPRESSEDGENES

One strategy for identifying genes that are involved in cardiovasculardisease is to detect genes that are expressed differentially underconditions associated with the disease versus non-disease conditions.The sub-sections below describe a number of experimental systems, calledparadigms, which may be used to detect such differentially expressedgenes. In general, the paradigms include at least one experimentalcondition in which subjects or samples are treated in a mannerassociated with cardiovascular disease, in addition to at least oneexperimental control condition lacking such disease associatedtreatment. Differentially expressed genes are detected, as describedherein, below, by comparing the pattern of gene expression between theexperimental and control conditions.

Once a particular gene has been identified through the use of one suchparadigm, its expression pattern may be further characterized bystudying its expression in a different paradigm. A gene may, forexample, be regulated one way in a given paradigm (e.g., up-regulation),but may be regulated differently in some other paradigm (e.g.,down-regulation). Furthermore, while different genes may have similarexpression patterns in one paradigm, their respective expressionpatterns may differ from one another under a different paradigm. Suchuse of multiple paradigms may be useful in distinguishing the roles andrelative importance of particular genes in cardiovascular disease.

5.1.1.1. FOAM CELL PARADIGM—1

Among the paradigms which may be utilized for the identification ofdifferentially expressed genes involved in atherosclerosis, for example,are paradigms designed to analyze those genes which may be involved infoam cell formation. Such paradigms may serve to identify genes involvedin the differentiation of this cell type, or their uptake of oxidizedLDL.

One embodiment of such a paradigm, hereinafter referred to as ParadigmA. First, human blood is drawn and peripheral monocytes are isolated bymethods routinely practiced in the art. These human monocytes can thenbe used immediately or cultured in vitro, using methods routinelypracticed in the art, for 5 to 9 days where they develop moremacrophage-like characteristics such as the up-regulation of scavengerreceptors. These cells are then treated for various lengths of time withagents thought to be involved in foam cell formation. These agentsinclude but are not limited to oxidized LDL, acetylated LDL,lysophosphatidylcholine, and homocysteine. Control monocytes that areuntreated or treated with native LDL are grown in parallel. At a certaintime after addition of the test agents, the cells are harvested andanalyzed for differential expression as described in detail in Section5.1.2., below. The Example presented in Section 6, below, demonstratesin detail the use of such a foam cell paradigm to identify genes whichare differentially expressed in treated versus control cells.

5.1.1.2. FOAM CELL PARADIGM—2

Alternative paradigms involving monocytes for detecting differentiallyexpressed genes associated with atherosclerosis involve the simulationof the phenomenon of transmigration. When monocytes encounter arterialinjury, they adhere to the vascular endothelial layer, transmigrateacross this layer, and locate between the endothelium and the layer ofsmooth muscle cells that ring the artery. This phenomenon can bemimicked in vitro by culturing a layer of endothelial cells isolated,for example, from human umbilical cord. Once the endothelial monolayerforms, monocytes drawn from peripheral blood are cultured on top of theendothelium in the presence and absence of LDL. After several hours, themonocytes transmigrate through the endothelium and develop into foamcells after 3 to 5 days when exposed to LDL. In this system, as in vivo,the endothelial cells carry out the oxidation of LDL which is then takenup by the monocytes. As described in sub-section 5.1.2. below, thepattern of gene expression can then be compared between these foam cellsand untreated monocytes.

5.1.1.3. FOAM CELL PARADIGM—3

Yet another system includes the third cell type, smooth muscle cell,that plays a critical role in atherogenesis (Navab et al., 1988, J.Clin. Invest., 82: 1853). In this system, a multilayer of human aorticsmooth muscle cells was grown on a micropore filter covered with a gellayer of native collagen, and a monolayer of human aortic endothelialcells was grown on top of the collagen layer. Exposure of this cocultureto human monocytes in the presence of chemotactic factor rFMLP resultedin monocyte attachment to the endothelial cells followed by migrationacross the endothelial monolayer into the collagen layer of thesubendothelial space. This type of culture can also be treated with LDLto generate foam cells. The foam cells can then be harvested and theirpattern of gene expression compared to that of untreated cells asexplained below in sub-section 5.1.2.

5.1.1.4. IN VIVO MONOCYTE PARADIGM

An alternative embodiment of such paradigms for the study of monocytes,hereinafter referred to as Paradigm B, involves differential treatmentof human subjects through the dietary control of lipid consumption. Suchhuman subjects are held on a low fat/low cholesterol diet for threeweeks, at which time blood is drawn, monocytes are isolated according tothe methods routinely practiced in the art, and RNA is purified, asdescribed below, in sub-section 5.1.2. These same patients aresubsequently switched to a high fat/high cholesterol diet and monocyteRNA is purified again. The patients may also be fed a third, combinationdiet containing high fat/low cholesterol and monocyte RNA may bepurified once again. The order in which patients receive the diets maybe varied. The RNA derived from patients maintained on two of the diets,or on all three diets, may then be compared and analyzed fordifferential gene expression as, explained below in sub-section 5.1.2.

The Example presented in Section 7, below, demonstrates the use of suchan in vivo monocyte paradigm to identify genes which are expresseddifferentially in monocytes of patients maintained on an atherogenicdiet versus their expression under a control diet. Such a paradigm mayalso be used in conjunction with an in vitro preliminary detectionsystem, as described in Section 7, below.

5.1.1.5. ENDOTHELIAL CELL—IL-1 PARADIGM

In addition to the detection of differential gene expression inmonocytes, paradigms focusing on endothelial cells may be used to detectgenes involved in cardiovascular disease. In one such paradigm,hereinafter referred to as Paradigm C, human umbilical vein endothelialcells (HUVEC's) are grown in vitro. Experimental cultures are treatedwith human IL-1β, a factor known to be involved in the inflammatoryresponse, in order to mimic the physiologic conditions involved in theatherosclerotic state. Alternatively experimental HUVEC cultures may betreated with lysophosphatidylcholine, a major phospholipid component ofatherogenic lipoproteins or oxidized human LDL. Control cultures aregrown in the absence of these compounds.

After a certain period of exposure treatment, experimental and controlcells are harvested and analyzed for differential gene expression asdescribed in sub-section 5.1.2, below. The Example presented in Section8, below, demonstrates the use of such an IL-1 induced endothelial cellparadigm to identify sequences which are differentially expressed intreated versus control cells.

5.1.1.6. ENDOTHELIAL CELL—SHEAR STRESS PARADIGM

In another paradigm involving endothelial cells, hereinafter referred toas Paradigm D, cultures are exposed to fluid shear stress which isthought to be responsible for the prevalence of atherosclerotic lesionsin areas of unusual circulatory flow. Unusual blood flow also plays arole in the harmful effects of ischemia/reperfusion, wherein an organreceiving inadequate blood supply is suddenly reperfused with anoverabundance of blood when the obstruction is overcome.

Cultured HUVEC monolayers are exposed to laminar sheer stress byrotating the culture in a specialized apparatus containing liquidculture medium (Nagel et al., 1994, J. Clin. Invest. 94: 885-891).Static cultures grown in the same medium serve as controls. After acertain period of exposure to shear stress, experimental and controlcells are harvested and analyzed for differential gene expression asdescribed in sub-section 5.1.2, below. The Example presented in Section9, below, demonstrates the use of such a shear stressed endothelial cellparadigm to identify sequences which are differentially expressed inexposed versus control cells.

In all such paradigms designed to identify genes which are involved incardiovascular disease, including but not limited to those describedabove in Sections 5.1.1.1 through 5.1.1.6, compounds such as drugs knownto have an ameliorative effect on the disease symptoms may beincorporated into the experimental system. Such compounds may includeknown therapeutics, as well as compounds that are not useful astherapeutics due to their harmful side effects. Test cells that arecultured as explained in the paradigms described in Sections 5.1.1.1through 5.1.1.6, for example, may be exposed to one of these compoundsand analyzed for differential gene expression with respect to untreatedcells, according to the methods described below in Section 5.1.2. Inprinciple, according to the particular paradigm, any cell type involvedin the disease may be treated at any stage of the disease process bythese compounds.

Test cells may also be compared to unrelated cells (e.g., fibroblasts)that are also treated with the compound, in order to screen out genericeffects on gene expression that might not be related to the disease.Such generic effects might be manifest by changes in gene expressionthat are common to the test cells and the unrelated cells upon treatmentwith the compound.

By these methods, the genes and gene products upon which these compoundsact can be identified and used in the assays described below to identifynovel therapeutic compounds for the treatment of cardiovascular disease.

5.1.2. ANALYSIS OF PARADIGM MATERIAL

In order to identify differentially expressed genes, RNA, either totalor mRNA, may be isolated from one or more tissues of the subjectsutilized in paradigms such as those described earlier in this Section.RNA samples are obtained from tissues of experimental subjects and fromcorresponding tissues of control subjects. Any RNA isolation techniquewhich does not select against the isolation of mRNA may be utilized forthe purification of such RNA samples. See, for example, Sambrook et al.,1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press,New York; and Ausubel, F. M. et al., eds., 1987-1993, Current Protocolsin Molecular Biology, John Wiley & Sons, Inc. New York, both of whichare incorporated herein by reference in their entirety. Additionally,large numbers of tissue samples may readily be processed usingtechniques well known to those of skill in the art, such as, forexample, the single-step RNA isolation process of Chomczynski, P. (1989,U.S. Pat. No. 4,843,155), which is incorporated herein by reference inits entirety.

Transcripts within the collected RNA samples which represent RNAproduced by differentially expressed genes may be identified byutilizing a variety of methods which are well known to those of skill inthe art. For example, differential screening (Tedder, T. F. et al.,1988, Proc. Natl. Acad. Sci. USA 85:208-212), subtractive hybridization(Hedrick, S. M. et al., 1984, Nature 308:149-153; Lee, S. W. et al.,1984, Proc. Natl. Acad. Sci. USA 88:2825), and, preferably, differentialdisplay (Liang, P., and Pardee, A. B., 1993, U.S. Pat. No. 5,262,311,which is incorporated herein by reference in its entirety), may beutilized to identify nucleic acid sequences derived from genes that aredifferentially expressed.

Differential screening involves the duplicate screening of a cDNAlibrary in which one copy of the library is screened with a total cellcDNA probe corresponding to the mRNA population of one cell type while aduplicate copy of the cDNA library is screened with a total cDNA probecorresponding to the mRNA population of a second cell type. For example,one cDNA probe may correspond to a total cell cDNA probe of a cell typederived from a control subject, while the second cDNA probe maycorrespond to a total cell cDNA probe of the same cell type derived froman experimental subject. Those clones which hybridize to one probe butnot to the other potentially represent clones derived from genesdifferentially expressed in the cell type of interest in control versusexperimental subjects.

Subtractive hybridization techniques generally involve the isolation ofmRNA taken from two different sources, e.g., control and experimentaltissue, the hybridization of the mRNA or single-stranded cDNAreverse-transcribed from the isolated mRNA, and the removal of allhybridized, and therefore double-stranded, sequences. The remainingnon-hybridized, single-stranded cDNAs, potentially represent clonesderived from genes that are differentially expressed in the two mRNAsources. Such single-stranded cDNAs are then used as the startingmaterial for the construction of a library comprising clones derivedfrom differentially expressed genes.

The differential display technique describes a procedure, utilizing thewell known polymerase chain reaction (PCR; the experimental embodimentset forth in Mullis, K. B., 1987, U.S. Pat. No. 4,683,202) which allowsfor the identification of sequences derived from genes which aredifferentially expressed. First, isolated RNA is reverse-transcribedinto single-stranded cDNA, utilizing standard techniques which are wellknown to those of skill in the art. Primers for the reversetranscriptase reaction may include, but are not limited to, oligodT-containing primers, preferably of the reverse primer type ofoligonucleotide described below. Next, this technique uses pairs of PCRprimers, as described below, which allow for the amplification of clonesrepresenting a random subset of the RNA transcripts present within anygiven cell. Utilizing different pairs of primers allows each of the mRNAtranscripts present in a cell to be amplified. Among such amplifiedtranscripts may be identified those which have been produced fromdifferentially expressed genes.

The reverse oligonucleotide primer of the primer pairs may contain anoligo dT stretch of nucleotides, preferably eleven nucleotides long, atits 5′ end, which hybridizes to the poly(A) tail of mRNA or to thecomplement of a cDNA reverse transcribed from an mRNA poly(A) tail.Second, in order to increase the specificity of the reverse primer, theprimer may contain one or more, preferably two, additional nucleotidesat its 3′ end. Because, statistically, only a subset of the mRNA derivedsequences present in the sample of interest will hybridize to suchprimers, the additional nucleotides allow the primers to amplify only asubset of the mRNA derived sequences present in the sample of interest.This is preferred in that it allows more accurate and completevisualization and characterization of each of the bands representingamplified sequences.

The forward primer may contain a nucleotide sequence expected,statistically, to have the ability to hybridize to cDNA sequencesderived from the tissues of interest. The nucleotide sequence may be anarbitrary one, and the length of the forward oligonucleotide primer may,range from about 9 to about 13 nucleotides, with about 10 nucleotidesbeing preferred. Arbitrary primer sequences cause the lengths of theamplified partial cDNAs produced to be variable, thus allowing differentclones to be separated by using standard denaturing sequencing gelelectrophoresis.

PCR reaction conditions should be chosen which optimize amplifiedproduct yield and specificity, and, additionally, produce amplifiedproducts of lengths which may be resolved utilizing standard gelelectrophoresis techniques. Such reaction conditions are well known tothose of-skill in the art, and important reaction parameters include,for example, length and nucleotide sequence of oligonucleotide primersas discussed above, and annealing and elongation step temperatures andreaction times.

The pattern of clones resulting from the reverse transcription andamplification of the mRNA of two different cell types is displayed viasequencing gel electrophoresis and compared. Differences in the twobanding patterns indicate potentially differentially expressed genes.

Once potentially differentially expressed gene sequences have beenidentified via bulk techniques such as, for example, those describedabove, the differential expression of such putatively differentiallyexpressed genes should be corroborated. Corroboration may beaccomplished via, for example, such well known techniques as Northernanalysis and/or RT-PCR.

Upon corroboration, the differentially expressed genes may be furthercharacterized, and may be identified as target and/or fingerprint genes,as discussed, below, in Section 5.3.

Also, amplified sequences of differentially expressed genes obtainedthrough, for example, differential display may be used to isolate fulllength clones of the corresponding gene. The full length coding portionof the gene may readily be isolated, without undue experimentation, bymolecular biological techniques well known in the art. For example, theisolated differentially expressed amplified fragment may be labeled andused to screen a cDNA library. Alternatively, the labeled fragment maybe used to screen a genomic library.

PCR technology may also be utilized to isolate full length cDNAsequences. As described, above, in this Section, the isolated, amplifiedgene fragments obtained through differential display have 5′ terminalends at some random point within the gene and have 3′ terminal ends at aposition preferably corresponding to the 3′ end of the transcribedportion of the gene. Once nucleotide sequence information from anamplified fragment is obtained, the remainder of the gene (i.e., the 5′end of the gene, when utilizing differential display) may be obtainedusing, for example, RT-PCR.

In one embodiment of such a procedure for the identification and cloningof full length gene sequences, RNA may be isolated, following standardprocedures, from an appropriate tissue or cellular source. A reversetranscription reaction may then be performed on the RNA using anoligonucleotide primer complimentary to the mRNA that corresponds to theamplified fragment, for the priming of first strand synthesis. Becausethe primer is anti-parallel to the mRNA, extension will proceed towardthe 5′ end of the mRNA. The resulting RNA/DNA hybrid may then be“tailed” with guanines using a standard terminal transferase reaction,the hybrid may be digested with RNAase H, and second strand synthesismay then be primed with a poly-C primer. Using the two primers, the 5′portion of the gene is amplified using PCR. Sequences obtained may thenbe isolated and recombined with previously isolated sequences togenerate a full-length cDNA of the differentially expressed genes of theinvention. For a review of cloning strategies and recombinant DNAtechniques, see e.g., Sambrook et al., 1989, supra; and Ausubel et al.,1989, supra.

5.2. IDENTIFICATION OF PATHWAY GENES

This section describes methods for the identification of genes, termed“pathway genes”, involved in cardiovascular disease. “Pathway gene”, asused herein, refers to a gene whose gene product exhibits the ability tointeract with gene products involved in cardiovascular disease. Apathway gene may be differentially expressed and, therefore, mayadditionally have the characteristics of a target and/or fingerprintgene.

Any method suitable for detecting protein-protein interactions may beemployed for identifying pathway gene products by identifyinginteractions between gene-products and gene products known to beinvolved in cardiovascular disease. Such known gene products may becellular or extracellular proteins. Those gene products which interactwith such known gene products represent pathway gene products and thegenes which encode them represent pathway genes.

Among the traditional methods which may be employed areco-immunoprecipitation, crosslinking and co-purification throughgradients or chromatographic columns. Utilizing procedures such as theseallows for the identification of pathway gene products. Once identified,a pathway gene product may be used, in conjunction with standardtechniques, to identify its corresponding pathway gene. For example, atleast a portion of the amino acid sequence of the pathway gene productmay be ascertained using techniques well known to those of skill in theart, such as via the Edman degradation technique (see, e.g., Creighton,1983, Proteins: Structures and Molecular Principles, W. H. Freeman &Co., New York, pp.34-49). The amino acid sequence obtained may be usedas a guide for the generation of oligonucleotide mixtures that can beused to screen for pathway gene sequences. Screening made beaccomplished, for example by standard hybridization or PCR techniques.Techniques for the generation of oligonucleotide mixtures and screeningare well-known. (See, e.g., Ausubel, supra., and PCR Protocols: A Guideto Methods and Applications, 1990, Innis, M. et al., eds. AcademicPress, Inc., New York).

Additionally, methods may be employed which result in the simultaneousidentification of pathway genes which encode the protein interactingwith a protein involved in cardiovascular disease. These methodsinclude, for example, probing expression libraries with labeled proteinknown or suggested to be involved in cardiovascular disease, using thisprotein in a manner similar to the well known technique of antibodyprobing of λgt11 libraries.

One such method which detects protein interactions in vivo, thetwo-hybrid system, is described in detail for illustration only and notby way of limitation. One version of this system has been described(Chien et al., 1991, Proc. Natl. Acad. Sci. USA, 88:9578-9582) and iscommercially available from Clontech (Palo Alto, Calif.).

Briefly, utilizing such a system, plasmids are constructed that encodetwo hybrid proteins: one consists of the DNA-binding domain of atranscription activator protein fused to a known protein, and the otherconsists of the activator protein's activation domain fused to anunknown protein that is encoded by a cDNA which has been recombined intothis plasmid as part of a cDNA library. The plasmids are transformedinto a strain of the yeast Saccharomyces cerevisiae that contains areporter gene (e.g., lacZ) whose, regulatory region contains theactivator's binding sites. Either hybrid protein alone cannot activatetranscription of the reporter gene, the DNA-binding domain hybridbecause it does not provide activation function and the activationdomain hybrid because it cannot localize to the activator's bindingsites. Interaction of the two proteins reconstitutes the functionalactivator protein and results in expression of the reporter gene, whichis detected by an assay for the reporter gene product.

The two-hybrid system or related methodology may be used to screenactivation domain libraries for proteins that interact with a known“bait” gene protein. Total genomic or cDNA sequences may be fused to theDNA encoding an activation domain. Such a library and a plasmid encodinga hybrid of the bait gene protein fused to the DNA-binding domain may becotransformed into a yeast reporter strain, and the resultingtransformants may be screened for those that express the reporter gene.These colonies may be purified and the library plasmids responsible forreporter gene expression may be isolated. DNA sequencing may then beused to identify the proteins encoded by the library plasmids.

For example, and not by way of limitation, the bait gene may be clonedinto a vector such that it is translationally fused to the DNA encodingthe DNA-binding domain of the GAL4 protein. Also by way of example, forthe isolation of genes involved in cardiovascular disease, previouslyisolated genes known or suggested to play a part in cardiovasculardisease may be used as the bait genes. These include but are not limitedto the genes for bFGF, IGF-I, VEGF, IL-1, M-CSF, TGFβ, TGFα, TNFα,HB-EGF, PDGF, IFN-γ, and GM-CSF, to name a few.

A cDNA library of the cell line from which proteins that interact withbait gene are to be detected can be made using methods routinelypracticed in the art. According to the particular system describedherein, for example, the cDNA fragments may be inserted into a vectorsuch that they are translationally fused to the activation domain ofGAL4. This library may be co-transformed along with the bait gene-GAL4fusion plasmid into a yeast strain which contains a lacZ gene driven bya promoter which contains the GAL4 activation sequence. A cDNA encodedprotein, fused to the GAL4 activation domain, that interacts with baitgene will reconstitute an active GAL4 protein and thereby driveexpression of the lacZ gene. Colonies which express lacZ may be detectedby their blue color in the presence of X-gal. The cDNA may then bepurified from these strains, and used to produce and isolate the baitgene-interacting protein using techniques routinely practiced in theart.

Once a pathway gene has been identified and isolated, it may be furthercharacterized as, for example, discussed below, in Section 5.3.

5.3. CHARACTERIZATION OF DIFFERENTIALLY EXPRESSED AND PATHWAY GENES

Differentially expressed genes, such as those identified via the methodsdiscussed, above, in Section 5.1.1, pathway genes, such as thoseidentified via the methods discussed, above, in Section 5.2, as well asgenes identified by alternative means, may be further characterized byutilizing, for example, methods such as those discussed herein. Suchgenes will be referred to herein as “identified genes”.

Analyses such as those described herein will yield information regardingthe biological function of the identified genes. An assessment of thebiological function of the differentially expressed genes, in addition,will allow for their designation as target and/or fingerprint genes.Specifically, any of the differentially expressed genes whose furthercharacterization indicates that a modulation of the gene's expression ora modulation of the gene product's activity may amelioratecardiovascular disease will be designated “target genes”, as defined,above, in Section 5.1. Such target genes and target gene products, alongwith those discussed below, will constitute the focus of the compounddiscovery strategies discussed, below, in Section 5.5.

Any of the differentially expressed genes whose further characterizationindicates that such modulations may not positively affect cardiovasculardisease, but whose expression pattern contributes to a gene expression“fingerprint pattern” correlative of, for example, a cardiovasculardisease condition will be designated a “fingerprint gene”. “Fingerprintpatterns” will be more fully discussed, below, in Section 5.8. It shouldbe noted that each of the target genes may also function as fingerprintgenes, as may all or a subset of the pathway genes.

It should further be noted that the pathway genes may also becharacterized according to techniques such as those described herein.Those pathway genes which yield information indicating that they aredifferentially expressed and that modulation of the gene's expression ora modulation of the gene product's activity may amelioratecardiovascular disease will be also be designated “target genes”. Suchtarget genes and target gene products, along with those discussed above,will constitute the focus of the compound discovery strategiesdiscussed, below, in Section 5.5.

It should be additionally noted that the characterization of one or moreof the pathway genes may reveal a lack of differential expression, butevidence that modulation of the gene's activity or expression may,nonetheless, ameliorate cardiovascular disease symptoms. In such cases,these genes and gene products would also be considered a focus of thecompound discovery strategies of Section 5.5, below.

In instances wherein a pathway gene's characterization indicates thatmodulation of gene expression or gene product activity may notpositively affect cardiovascular disease, but whose expression isdifferentially expressed and which contributes to a gene expressionfingerprint pattern correlative of, for example, a cardiovasculardisease state, such pathway genes may additionally be designated asfingerprint genes.

Among the techniques whereby the identified genes may be furthercharacterized, the nucleotide sequence of the identified genes, whichmay be obtained by utilizing standard techniques well known to those ofskill in the art, may be used to further characterize such genes. Forexample, the sequence of the identified genes may reveal homologies toone or more known sequence motifs which may yield information regardingthe biological function of the identified gene product.

Second, an analysis of the tissue distribution of the mRNA produced bythe identified genes may be conducted, utilizing standard techniqueswell known to those of skill in the art. Such techniques may include,for example, Northern analyses and RT-PCR. Such analyses provideinformation as to whether the identified genes are expressed in tissuesexpected to contribute to cardiovascular disease. Such analyses may alsoprovide quantitative information regarding steady state mRNA regulation,yielding data concerning which of the identified genes exhibits a highlevel of regulation in, preferably, tissues which may be expected tocontribute to cardiovascular disease.

Such analyses may also be performed on an isolated cell population of aparticular cell type derived from a given tissue. Additionally, standardin situ hybridization techniques may be utilized to provide informationregarding which cells within a given tissue express the identified gene.Such analyses may provide information regarding the biological functionof an identified gene relative to cardiovascular disease in instanceswherein only a subset of the cells within the tissue is thought to berelevant to cardiovascular disease.

Third, the sequences of the identified genes may be used, utilizingstandard techniques, to place the genes onto genetic maps, e.g., mouse(Copeland & Jenkins, 1991, Trends. in Genetics 7: 113-118) and humangenetic maps (Cohen, et al., 1993, Nature 366: 698-701). Such mappinginformation may yield information regarding the genes' importance tohuman disease by, for example, identifying genes which map near geneticregions to which known genetic cardiovascular disease tendencies map.

Fourth, the biological function of the identified genes may be moredirectly assessed by utilizing relevant in vivo and in vitro systems. Invivo systems may include, but are not limited to, animal systems whichnaturally exhibit cardiovascular disease predisposition, or ones whichhave been engineered to exhibit such symptoms, including but not limitedto the apoE-deficient atherosclerosis mouse model (Plump et al., 1992,Cell 71: 343-353). Such systems are discussed in Section 5.4.4.1, below.

The use of such an in vivo system is described in detail in the exampleprovided in Section 7, below, confirming the role of the target genebcl-2 (see Table 1, in Section 5.4.1, below). Briefly, bcl-2 expressionfirst was shown to be down-regulated in the apoE-deficientatherosclerosis mouse model. Then, a transgenic mouse was engineeredbearing the human bcl-2 gene under the control of a promoter which isinduced in monocyte foam cells under atherogenic conditions. To test theeffect of the induction of bcl-2 under such conditions, the transgenicmouse is crossed with the apoE-deficient mouse. apoE-deficient progenybearing the highly expressible bcl-2 gene are then examined for plaqueformation and development. Reduction in plaque formation and developmentin these progeny confirms the effectiveness of intervening incardiovascular disease through this target gene.

In vitro systems may include, but are not limited to, cell-based systemscomprising cell types known or suspected of involvement incardiovascular disease. Such systems are discussed in detail, below, inSection 5.4.4.2.

In further characterizing the biological function of the identifiedgenes, the expression of these genes may be modulated within the in vivoand/or in vitro systems, i.e., either over- or underexpressed, and thesubsequent effect on the system then assayed. Alternatively, theactivity of the product of the identified gene may be modulated byeither increasing or decreasing the level of activity in the in vivoand/or in vitro system of interest, and its subsequent effect thenassayed.

The information obtained through such characterizations may suggestrelevant methods for the treatment of cardiovascular disease involvingthe gene of interest. For example, treatment may include a modulation ofgene expression and/or gene product activity. Characterizationprocedures such as those described herein ay indicate where suchmodulation should involve an increase or a decrease in the expression oractivity of the gene or gene product of interest. Such methods oftreatment are discussed, below, in Section 5.5.4.

5.4. DIFFERENTIALLY EXPRESSED AND PATHWAY GENES

Identified genes, which include but are not limited to differentiallyexpressed genes such as those identified in Section 5.1.1, above, andpathway genes, such as those identified in Section 5.2, above, aredescribed herein. Specifically, the nucleic acid sequences and geneproducts of such identified genes are described herein. Further,antibodies directed against the identified genes' products, and cell-and animal-based models by which the identified genes may be furthercharacterized and utilized are also discussed in this Section.

5.4.1. DIFFERENTIALLY EXPRESSED AND PATHWAY GENE SEQUENCES

The differentially expressed and pathway genes of the invention arelisted below, in Table 1. Differentially expressed and pathway genenucleotide sequences are shown in FIGS. 8, 12, 15, 22, 27A-D, 30A-K, and34A-D.

Table 1 lists differentially expressed genes identified through, forexample, the paradigms discussed, above, in Section 5.1.1, and below, inthe examples presented in Sections 6 through 9. Table 1 also summarizesinformation regarding the further characterization of such genes.

First, the paradigm used initially to detect the differentiallyexpressed gene is described under the column headed “Paradigm ofOriginal Detection”. The expression patterns of those genes which havebeen shown to be differentially expressed, for example, under one ormore of the paradigm conditions described in Section 5.1.1 aresummarized under the column headed “Paradigm Expression Pattern”. Foreach of the tested genes, the paradigm which was used and the differencein the expression of the gene among the samples generated is shown. “↑”indicates that gene expression is up-regulated (i.e., there is anincrease in the amount of detectable mRNA) among the samples generated,while “↓” indicates that gene expression is down-regulated (i.e., thereis a decrease in the amount of detectable mRNA) among the samplesgenerated. “Detectable” as used herein, refers to levels of mRNA whichare detectable via, for example, standard Northern and/or RT-PCRtechniques which are well known to those of skill in the art.

Cell types in which differential expression was detected are alsosummarized in Table 1 under the column headed “Cell Type Detected in”.The column headed “Chromosomal Location” provides the human chromosomenumber on which the gene is located. Additionally, in instances whereinthe genes contain nucleotide sequences similar or homologous tosequences found in nucleic acid databases, references to suchsimilarities are listed.

The genes listed in Table 1 may be obtained using cloning methods wellknown to those skilled in the art, including but not limited to the useof appropriate probes to detect the genes within an appropriate cDNA orgDNA (genomic DNA) library. (See, for example, Sambrook et al., 1989,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories,which is incorporated by reference herein in its entirety). Probes forthe novel sequences reported herein may be obtained directly from theisolated clones deposited with the NRRL, as indicated in Table 2, below.Alternatively, oligonucleotide probes for the novel genes may besynthesized based on the DNA sequences disclosed herein in FIGS. 8, 12,15, 18, 22, 27A-D, 30A-K, and 34A-D. Such synthetic oligonucleotides maybe similarly produced based on the sequences provided for the previouslyknown genes described in the following references: Cleary et al., 1986,Cell 47: 19-28 (bcl-2); Takahashi et al., 1990, J. Biochem 108: 145-148(glutathione peroxidase); and Jones et al., 1993, J. Biol. Chem. 268:9049-9054 (prostaglandin endoperoxide synthase II), each of which isincorporated herein in its entirety.

The sequence obtained from clones containing partial coding sequences ornon-coding sequences can be used to obtain the entire coding region byusing the RACE method (Chenchik, et al., 1995, CLONTECHniques (X) 1:5-8; Barnes, 1994, Proc. Natl. Acad. Sci. USA 91: 2216-2220; and Chenget al., Proc. Natl. Acad. Sci. USA 91: 5695-5699). Oligonucleotides canbe designed based on the sequence obtained from the partial clone thatcan amplify a reverse transcribed mRNA encoding the entire codingsequence. This method was used, as described in the example in Section9, below, to obtain the entire coding region of the rchd523 gene.

Alternatively, probes can be used to screen cDNA libraries prepared froman appropriate cell or cell line in which the gene is transcribed. Forexample, the genes described herein that were detected in monocytes maybe cloned from a cDNA library prepared from monocytes isolated asdescribed in Section 7.1.1, below. In fact, as described in detail inthe example in Section 9, below, this method was applied in order toobtain the entire coding region of the rchd534 gene. Briefly, theup-regulation of this gene was detected, under Paradigm D, in HUVEC'ssubjected to shear stress. Then, amplified partial sequence of therchd534 gene was subcloned. The insert was then isolated and used toprobe a cDNA library prepared from shear stress treated HUVEC's. A cDNAclone containing the entire rchd534 coding region was detected,isolated, and sequenced.

The genes described herein that were detected in endothelial cells mayalso be cloned from a cDNA library constructed from endothelial cellsisolated as described in Progress in Hemostasis and Thrombosis, Vol. 3,P. Spaet, editor, Grune & Stratton Inc., New York, 1-28. Alternatively,the genes may be retrieved from a human placenta cDNA library (ClontechLaboratories, Palo Alto, Calif.), according to Takahashi et al., 1990,supra; a HUVEC cDNA library as described in Jones et al. 1993, supra; oran acute lymphoblastic leukemia (SUP-B2) cDNA library as described inCleary et al., 1986, supra, for example. Genomic DNA libraries can beprepared from any source.

TABLE 1 Differentially Expressed and Pathway Genes Paradigm Paradigm ofExpr. Cell Type Chromosoma Gene Seq. ID # Original Detection PatternDetected in 1 Location Ref Seq. Band 14: B ⇓ Monocytes 1 bcl-2 (Section5.1.1.4) Glutathione B ⇓ Monocytes 2 peroxidase rchd005 1 C EndothelialNew 3 FIG. 8 (Section 5.1.1.5) rchd024 2 C Endothelial  4 New FIG. 12rchd032 3 C Endothelial New FIG. 15 rchd036 4 C Endothelial 15 New FIG.18 rchd502 5 D Endothelial New 4 FIG. 22 (Section 5.1.1.6) rchd505: DEndothelial 5 Endoperoxide synthase rchd523 6 D Endothelial  7 New FIGS.27A-B rchd528 7 D Endothelial New FIG. 30 rchd534 36  D Endothelial 15New FIGS. 34A-B 1 Cleary et al., 1986, Cell 47:19-28. 2 Takahashi etal., 1990, J. Biochem. 108:145-148. 3 Shark Na—K—Cl cotransporter, Xu etal., 1994 Proc. Natl. Acad. Sci. U.S.A. 91:2201-2205. 4 Rat matrin F/G,Hakes et al., 1991 Proc. Natl. Acad. Sci. U.S.A. 88:6186-6190. 5 Joneset al., 1993, J. Biol. Chem. 268:9049-9054.

Table 2, below, lists isolated clones that contain sequences of thenovel genes listed in Table 1. Such clones were produced from amplifiedsequences of the indicated differential display band which weresubcloned into the TA cloning vector (Invitrogen, San Diego, Calif.), asdescribed in Section 6.1, below. Also listed in Table 2, below, are thestrains deposited with the NRRL which contain each such clone. Suchstrains were produced by transforming E. coli strain INVαF′ (Invitrogen)with the indicated plasmid, as described in Section 6.1, below. Thenames of the plasmids containing the entire coding region of a novelgene bear the prefix pFCHD, and the names of the strains carrying theseplasmids bear the prefix FCHD.

TABLE 2 Plasmid Clone Strain Deposited Contained within GENE with NRRLDeposited Strain rchd005 RCHD005 pRCHD005 rchd024 RCHD024 pRCHD024rchd032 RCHD032 pRCHD032 rchd036 RCHD036 pRCHD036 rchd502 RCHD502pRCHD502 rchd523 FCHD523 pFCHD523 RCDH523 pRCHD523 rchd528 RCHD528pRCHD528 rchd534 FCHD534 pFCHD534

As used herein, “differentially expressed gene” (i.e. target andfingerprint gene) or “pathway gene” refers to (a) a gene containing atleast one of the DNA sequences disclosed herein (as shown in FIGS. 8,12, 15, 18, 22, 27A-D, 30A-K, and 34A-D), or contained in the cloneslisted in Table 2, as deposited with the NRRL; (b) any DNA sequence thatencodes the amino acid sequence encoded by the DNA sequences disclosedherein (as shown in FIGS. 8, 12, 15, 18, 22, 27A-D, 30A-K, and 34A-D),contained in the clones, listed in Table 2, as deposited with the NRRLor contained within the coding region of the gene to which the DNAsequences disclosed herein (as shown in FIGS. 8, 12, 15, 18, 22, 27A-D,30A-K, and 34A-D) or contained in the clones listed in Table 2, asdeposited with the NRRL, belong; (c) any DNA sequence that hybridizes tothe complement of the coding sequences disclosed herein, contained inthe clones listed in Table 2, as deposited with the NRRL, or containedwithin the coding region of the gene to which the DNA sequencesdisclosed herein (as shown in FIGS. 8, 12, 15, 18, 22, 27A-D, 30A-K, and34A-D) or contained in the clones listed in Table 2, as deposited withthe NRRL, belong, under highly stringent conditions, e.g., hybridizationto filter-bound DNA in 0.5 M NaHPO₄7% sodium dodecyl sulfate (SDS), 1 mMEDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C. (Ausubel F. M.et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I,Green Publishing Associates, Inc., and John Wiley & sons, Inc., NewYork, at p. 2.10.3) and encodes a gene product functionally equivalentto a gene product encoded by sequences contained within the cloneslisted in Table 2; and/or (d) any DNA sequence that hybridizes to thecomplement of the coding sequences disclosed herein, (as shown in FIGS.8, 12, 15, 18, 27A-D, 30A-K, and 34A-D) contained in the clones listedin Table 2, as deposited with the NRRL or contained within the codingregion of the gene to which DNA sequences disclosed herein (as shown inFIGS. 8, 12, 15, 18, 22, 27A-D, 30A-K, and 34A-D) or contained in theclones, listed in Table 2, as deposited with the NRRL, belong, underless stringent conditions, such as moderately stringent conditions,e.g., washing in 0.2×SSC/0.1% SDS at 42° C. (Ausubel et al., 1989,supra), yet which still encodes a functionally equivalent gene product.

The invention also includes nucleic acid molecules, preferably DNAmolecules, that hybridize to, and are therefore the complements of, theDNA sequences (a) through (c), in the preceding paragraph. Suchhybridization conditions may be highly stringent or less highlystringent, as described above. In instances wherein the nucleic acidmolecules are deoxyoligonucleotides (“oligos”), highly stringentconditions may refer, e.g., to washing in 6×SSC/0.05% sodiumpyrophosphate at 37° C. (for 14-base oligos), 48° C. (for 17-baseoligos), 55° C. (for 20-base oligos), and 60° C. (for 23-base oligos).These nucleic acid molecules may act as target gene antisense molecules,useful, for example, in target gene regulation and/or as antisenseprimers in amplification reactions of target gene nucleic acidsequences. Further, such sequences may be used as part of ribozymeand/or triple helix sequences, also useful for target gene regulation.Still further, such molecules may be used as components of diagnosticmethods whereby the presence of a cardiovascular disease-causing allele,may be detected.

The invention also encompasses (a) DNA vectors that contain any of theforegoing coding sequences and/or their complements (i.e., antisense);(b) DNA expression vectors that contain any of the foregoing codingsequences operatively associated with a regulatory element that directsthe expression of the coding sequences; and (c) genetically engineeredhost cells that contain any of the foregoing coding sequencesoperatively associated with a regulatory element that directs theexpression of the coding sequences in the host cell. As used herein,regulatory elements include but are not limited to inducible andnon-inducible promoters, enhancers, operators and other elements knownto those skilled in the art that drive and regulate expression. Theinvention includes fragments of any of the DNA sequences disclosedherein.

In addition to the gene sequences described above, homologues of suchsequences, as may, for example be present in other species, may beidentified and may be readily isolated, without undue experimentation,by molecular biological techniques well known in the art. Further, theremay exist genes at other genetic loci within the genome that encodeproteins which have extensive homology to one or more domains of suchgene products. These genes may also be identified via similartechniques.

For example, the isolated differentially expressed gene sequence may belabeled and used to screen a cDNA library constructed from RNA obtainedfrom the organism of interest. Hybridization conditions will be of alower stringency when the cDNA library was derived from an organismdifferent from the type of organism from which the labeled sequence wasderived. Alternatively, the labeled fragment may be used to screen agenomic library derived from the organism of interest, again, usingappropriately stringent conditions. Such low stringency conditions willbe well known to those of skill in the art, and will vary predictablydepending on the specific organisms from which the library and thelabeled sequences are derived. For guidance regarding such conditionssee, for example, Sambrook et al., 1989, Molecular Cloning, A LaboratoryManual, Cold Springs Harbor Press, New York; and Ausubel et al., 1989,Current Protocols in Molecular Biology, Green Publishing Associates andWiley Interscience, New York.

Further, a previously unknown differentially expressed or pathwaygene-type sequence may be isolated by performing PCR using twodegenerate oligonucleotide primer pools designed on the basis of aminoacid sequences within the gene of interest. The template for thereaction may be cDNA obtained by reverse transcription of mRNA preparedfrom human or non-human cell lines or tissue known or suspected toexpress a differentially expressed or pathway gene allele.

The PCR product may be subcloned and sequenced to insure that theamplified sequences represent the sequences of a differentiallyexpressed or pathway gene-like nucleic acid sequence. The PCR fragmentmay then be used to isolate a full length cDNA clone by a variety ofmethods. For example, the amplified fragment may be labeled and used toscreen a bacteriophage cDNA library. Alternatively, the labeled fragmentmay be used to screen a genomic library.

PCR technology may also be utilized to isolate full length cDNAsequences. For example, RNA may be isolated, following standardprocedures, from an appropriate cellular or tissue source. A reversetranscription reaction may be performed on the RNA using anoligonucleotide primer specific for the most 5′ end of the amplifiedfragment for the priming of first strand synthesis. The resultingRNA/DNA hybrid may then be “tailed” with guanines using a standardterminal transferase reaction, the hybrid may be digested with RNAase H,and second strand synthesis may then be primed with a poly-C primer.Thus, cDNA sequences upstream of the amplified fragment may easily beisolated. For a review of cloning strategies which may be used, seee.g., Sambrook et al., 1989, supra.

In cases where the differentially expressed or pathway gene identifiedis the normal, or wild type, gene, this gene may be used to isolatemutant alleles of the gene. Such an isolation is preferable in processesand disorders which are known or suspected to have a genetic basis.Mutant alleles may be isolated from individuals either known orsuspected to have a genotype which contributes to cardiovascular diseasesymptoms. Mutant alleles and mutant allele products may then be utilizedin the therapeutic and diagnostic assay systems described below.

A cDNA of the mutant gene may be isolated, for example, by using PCR, atechnique which is well known to those of skill in the art. In thiscase, the first cDNA strand may be synthesized by hybridizing anoligo-dT oligonucleotide to mRNA isolated from tissue known or suspectedto be expressed in an individual putatively carrying the mutant allele,and by extending the new strand with reverse transcriptase. The secondstrand of the cDNA is then synthesized using an oligonucleotide thathybridizes specifically to the 5′ end of the normal gene. Using thesetwo primers, the product is then amplified via PCR, cloned into asuitable vector, and subjected to DNA sequence analysis through methodswell known to those of skill in the art. By comparing the DNA sequenceof the mutant gene to that of the normal gene, the mutations)responsible for the loss or alteration of function of the mutant geneproduct can be ascertained.

Alternatively, a genomic or cDNA library can be constructed and screenedusing DNA or RNA, respectively, from a tissue known to or suspected ofexpressing the gene of interest in an individual suspected of or knownto carry the mutant allele. The normal gene or any suitable fragmentthereof may then be labeled and used as a probed to identify thecorresponding mutant allele in the library. The clone containing thisgene may then be purified through methods routinely practiced in theart, and subjected to sequence analysis as described, above, in thisSection.

Additionally, an expression library can be constructed utilizing DNAisolated from or cDNA synthesized from a tissue known to or suspected ofexpressing the gene of interest in an individual suspected of or knownto carry the mutant allele. In this manner, gene products made by theputatively mutant tissue may be expressed and screened using standardantibody screening techniques in conjunction with antibodies raisedagainst the normal gene product, as described, below, in Section 5.4.3.(For screening techniques, see, for example, Harlow, E. and Lane, eds.,1988, “Antibodies: A Laboratory Manual”, Cold Spring Harbor Press, ColdSpring Harbor.) In cases where the mutation results in an expressed geneproduct with altered function (e.g., as a result of a missensemutation), a polyclonal set of antibodies are likely to cross-react withthe mutant gene product. Library clones detected via their reaction withsuch labeled antibodies can be purified and subjected to sequenceanalysis as described in this Section, above.

5.4.2. DIFFERENTIALLY EXPRESSED AND PATHWAY GENE PRODUCTS

Differentially expressed and pathway gene products include thoseproteins encoded by the differentially expressed and pathway genesequences described in Section 5.4.1, above. Specifically,differentially expressed and pathway gene products may includedifferentially expressed and pathway gene polypeptides encoded by thedifferentially expressed and pathway gene sequences contained in theclones listed in Table 2, above, as deposited with the NRRL, orcontained in the coding regions of the genes to which DNA sequencesdisclosed herein (in FIGS. 8, 12, 15, 18, 22, 27A-D, 30A-K, and 34A-D)or contained in the clones, listed in Table 2, as deposited with theNRRL, belong, for example.

In addition, differentially expressed and pathway gene products mayinclude proteins that represent functionally equivalent gene products.Such an equivalent differentially expressed or pathway gene product maycontain deletions, additions or substitutions of amino acid residueswithin the amino acid sequence encoded by the differentially expressedor pathway gene sequences described, above, in Section 5.4.1, but whichresult in a silent change, thus producing a functionally equivalentdifferentially expressed on pathway gene product. Amino acidsubstitutions may be made on the basis of similarity in polarity,charge, solubility, hydrophobicity, hydrophilicity, and/or theamphipathic nature of the residues involved.

For example, nonpolar (hydrophobic) amino acids include alanine,leucine, isoleucine, valine, proline, phenylalanine, tryptophan, andmethionine; polar neutral amino acids include glycine, serine,threonine, cysteine, tyrosine, asparagine, and glutamine; positivelycharged (basic) amino acids include arginine, lysine, and histidine; andnegatively charged (acidic) amino acids include aspartic acid andglutamic acid. “Functionally equivalent”, as utilized herein, refers toa protein capable of exhibiting a substantially similar in vivo activityas the endogenous differentially expressed or pathway gene productsencoded by the differentially expressed or pathway gene sequencesdescribed in Section 5.4.1, above. Alternatively, when utilized as partof assays such as those described, below, in Section 5.5, “functionallyequivalent” may refer to peptides capable of interacting with othercellular or extracellular molecules in a manner substantially similar tothe way in which the corresponding portion of the endogenousdifferentially expressed or pathway gene product would.

The differentially expressed or pathway gene products may be produced byrecombinant DNA technology using techniques well known in the art. Thus,methods for preparing the differentially expressed or pathwaypolypeptides and peptides of the invention by expressing nucleic acidencoding differentially expressed or pathway gene sequences aredescribed herein. Methods which are well known to those skilled in theart can be used to construct expression vectors containingdifferentially expressed or pathway gene protein coding sequences andappropriate transcriptional/translational control signals. These methodsinclude, for example, in vitro recombinant DNA techniques, synthetictechniques and in vivo recombination/genetic recombination. See, forexample, the techniques described in Sambrook et al., 1989, supra, andAusubel et al., 1989, supra. Alternatively, RNA capable of encodingdifferentially expressed or pathway gene protein sequences may bechemically synthesized using, for example, synthesizers. See, forexample, the techniques described in “Oligonucleotide Synthesis”, 1984,Gait, M. J. ed., IRL Press, Oxford, which is incorporated by referenceherein in its entirety.

A variety of host-expression vector systems may be utilized to expressthe differentially expressed or pathway gene coding sequences of theinvention. Such host-expression systems represent vehicles by which thecoding sequences of interest may be produced and subsequently purified,but also represent cells which may, when transformed or transfected withthe appropriate nucleotide coding sequences, exhibit the differentiallyexpressed or pathway gene protein of the invention in situ. Theseinclude but are not limited to microorganisms such as bacteria (e.g., E.coli, B. subtilis) transformed with recombinant bacteriophage DNA,plasmid DNA or cosmid DNA expression vectors containing differentiallyexpressed or pathway gene protein coding sequences; yeast (e.g.Saccharomyces, Pichia) transformed with recombinant yeast expressionvectors containing the differentially expressed or pathway gene proteincoding sequences; insect cell systems infected with recombinant virusexpression vectors (e.g., baculovirus) containing the differentiallyexpressed or pathway gene protein coding sequences; plant cell systemsinfected with recombinant virus expression vectors (e.g., cauliflowermosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed withrecombinant plasmid expression vectors (e.g., Ti plasmid) containingdifferentially expressed or pathway gene protein coding sequences; ormammalian cell systems (e.g. COS, CHO, BHK, 293, 3T3) harboringrecombinant expression constructs containing promoters derived from thegenome of mammalian cells (e.g., metallothionein promoter) or frommammalian viruses (e.g., the adenovirus late promoter; the vacciniavirus 7.5K promoter).

In bacterial systems, a number of expression vectors may beadvantageously selected depending upon the use intended for thedifferentially expressed or pathway gene protein being expressed. Forexample, when a large quantity of such a protein is to be produced, forthe generation of antibodies or to screen peptide libraries, forexample, vectors which direct the expression of high levels of fusionprotein products that are readily purified may be desirable. Suchvectors include, but are not limited, to the E. coli expression vectorpUR278 (Ruther et al., 1983, EMBO J. 2:1791), in which thedifferentially expressed or pathway gene protein coding sequence may beligated individually into the vector in frame with the lac Z codingregion so that a fusion protein is produced; pIN vectors (Inouye &Inouye, 1985, Nucleic Acids Res. 13:3101-3109; Van Heeke & Schuster,1989, J. Biol. Chem. 264:5503-5509); and the like. PGEX vectors may alsobe used to express foreign polypeptides as fusion proteins withglutathione S-transferase (GST). In general, such fusion proteins aresoluble and can easily be purified from lysed cells by adsorption toglutathione-agarose beads followed by elution in the presence of freeglutathione. The pGEX vectors are designed to include thrombin or factorXa protease cleavage sites so that the cloned target gene protein can bereleased from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus(AcNPV) is used as a vector to express foreign genes. The virus grows inSpodoptera frugiperda cells. The differentially expressed or pathwaygene coding sequence may be cloned individually into non-essentialregions (for example the polyhedrin gene) of the virus and placed undercontrol of an AcNPV promoter (for example the polyhedrin promoter).Successful insertion of differentially expressed or pathway gene codingsequence will result in inactivation of the polyhedrin gene andproduction of non-occluded recombinant virus (i.e., virus lacking theproteinaceous coat coded for by the polyhedrin gene). These recombinantviruses are then used to infect Spodoptera frugiperda cells in which theinserted gene is expressed. (E.g., see Smith et al., 1983, J. Virol. 46:584; Smith, U.S. Pat. No. 4,215,051).

In mammalian host cells, a number of viral-based expression systems maybe utilized. In cases where an adenovirus is used as an expressionvector, the differentially expressed or pathway gene coding sequence ofinterest may be ligated to an adenovirus transcription/translationcontrol complex, e.g., the late promoter and tripartite leader sequence.This chimeric gene may then be inserted in the adenovirus genome by invitro or in vivo recombination. Insertion in a non-essential region ofthe viral genome (e.g., region E1 or E3) will result in a recombinantvirus that is viable and capable of expressing differentially expressedor pathway gene protein in infected hosts. (E.g., See Logan & Shenk,1984, Proc. Natl. Acad. Sci. USA 81:3655-3659). Specific initiationsignals may also be required for efficient translation of inserteddifferentially expressed or pathway gene coding sequences. These signalsinclude the ATG initiation codon and adjacent sequences. In cases wherean entire differentially expressed or pathway gene, including its owninitiation codon and adjacent sequences, is inserted into theappropriate expression vector, no additional translational controlsignals may be needed. However, in cases where only a portion of thedifferentially expressed or pathway gene coding sequence is inserted,exogenous translational control signals, including, perhaps, the ATGinitiation codon, must be provided. Furthermore, the initiation codonmust be in phase with the reading frame of the desired coding sequenceto ensure translation of the entire insert. These exogenoustranslational control signals and initiation codons can be of a varietyof origins, both natural and synthetic. The efficiency of expression maybe enhanced by the inclusion of appropriate transcription enhancerelements, transcription terminators, etc. (see Bittner et al., 1987,Methods in Enzymol. 153:516-544).

In addition, a host cell strain may be chosen which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Such modifications (e.g.,glycosylation) and processing (e.g., cleavage) of protein products maybe important for the function of the protein. Different host cells havecharacteristic and specific mechanisms for the post-translationalprocessing and modification of proteins. Appropriate cell lines or hostsystems can be chosen to ensure the correct modification and processingof the foreign protein expressed. To this end, eukaryotic host cellswhich possess the cellular machinery for proper processing of theprimary transcript, glycosylation, and phosphorylation of the geneproduct may be used. Such mammalian host cells include but are notlimited to CHO, VERO, BHK, HeLa, COS, MDCK, 293, 3T3, WI38, etc.

For long-term, high-yield production of recombinant proteins, stableexpression is preferred. For example, cell lines which stably expressthe differentially expressed or pathway gene protein may be engineered.Rather than using expression vectors which contain viral origins ofreplication, host cells can be transformed with DNA controlled byappropriate expression control elements (e.g., promoter, enhancer,sequences, transcription terminators, polyadenylation sites, etc.), anda selectable marker. Following the introduction of the foreign DNA,engineered cells may be allowed to grow for 1-2 days in an enrichedmedia, and then are switched to a selective media. The selectable markerin the recombinant plasmid confers resistance to the selection andallows cells to stably integrate the plasmid into their chromosomes andgrow to form foci which in turn can be cloned and expanded into celllines. This method may advantageously be used to engineer cell lineswhich express the differentially expressed or pathway gene protein. Suchengineered cell lines may be particularly useful in screening andevaluation of compounds that affect the endogenous activity of thedifferentially expressed or pathway gene protein.

A number of selection systems may be used, including but not limited tothe herpes simplex virus thymidine kinase (Wigler, et al., 1977, Cell11:223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska &Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48:2026), and adeninephosphoribosyltransferase (Lowy, et al., 1980, Cell 22:817) genes can beemployed in tk⁻, hgprt⁻ or aprt⁻ cells, respectively. Also,antimetabolite resistance can be used as the basis of selection fordhfr, which confers resistance to methotrexate (Wigler, et al., 1980,Natl. Acad. Sci. USA 77:3567; O'Hare, et al., 1981, Proc. Natl. Acad.Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid(Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, whichconfers resistance to the aminoglycoside G-418 (Colberre-Garapin, etal., 1981, J. Mol. Biol. 150:1); and hygro, which confers resistance tohygromycin (Santerre, et al., 1984, Gene 30:147) genes.

An alternative fusion protein system allows for the ready purificationof non-denatured fusion proteins expressed in human cell lines(Janknecht, et al., 1991, Proc. Natl. Acad. Sci. USA 88: 8972-8976). Inthis system, the gene of interest is subcloned into a vacciniarecombination plasmid such that the gene's open reading frame istranslationally fused to an amino-terminal tag consisting of sixhistidine residues. Extracts from cells infected with recombinantvaccinia virus are loaded onto Ni²⁻ nitriloacetic acid-agarose columnsand histidine-tagged proteins are selectively eluted withimidazole-containing buffers.

When used as a component in assay systems such as those described,below, in Section 5.5, the differentially expressed or pathway geneprotein may be labeled, either directly or indirectly, to facilitatedetection of a complex formed between the differentially expressed orpathway gene protein and a test substance. Any of a variety of suitablelabeling systems may be used including but not limited to radioisotopessuch as ¹²⁵I; enzyme labelling systems that generate a detectablecalorimetric signal or light when exposed to substrate; and fluorescentlabels.

Where recombinant DNA technology is used to produce the differentiallyexpressed or pathway gene protein for such assay systems, it may beadvantageous to engineer fusion proteins that can facilitate labeling,immobilization and/or detection.

Indirect labeling involves the use of a protein, such as a labeledantibody, which specifically binds to either a differentially expressedor pathway gene product. Such antibodies include but are not limited topolyclonal, monoclonal, chimeric, single chain, Fab fragments andfragments produced by an Fab expression library.

5.4.3. DIFFERENTIALLY EXPRESSED OR PATHWAY GENE PRODUCT ANTIBODIES

Described herein are methods for the production of antibodies capable ofspecifically recognizing one or more differentially expressed or pathwaygene epitopes. Such antibodies may include, but are not limited topolyclonal antibodies, monoclonal antibodies (mAbs), humanized orchimeric antibodies, single chain antibodies, Fab fragments, F(ab′)₂fragments, fragments produced by a Fab expression library,anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments ofany of the above. Such antibodies may be used, for example, in thedetection of a fingerprint, target, or pathway gene in a biologicalsample, or, alternatively, as a method for the inhibition of abnormaltarget gene activity. Thus, such antibodies may be utilized as part ofcardiovascular disease treatment methods, and/or may be used as part ofdiagnostic techniques whereby patients may be tested for abnormal levelsof fingerprint, target, or pathway gene proteins, or for the presence ofabnormal forms of the such proteins.

For the production of antibodies to a differentially expressed orpathway gene, various host animals may be immunized by injection with adifferentially expressed or pathway gene protein, or a portion thereof.Such host animals may include but are not limited to rabbits, mice, andrats, to name but a few. Various adjuvants may be used to increase theimmunological response, depending on the host species, including but notlimited to Freund's (complete and incomplete), mineral gels such asaluminum hydroxide, surface active substances such as lysolecithin,pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpethemocyanin, dinitrophenol, and potentially useful human adjuvants suchas BCG (bacille Calmette-Guerin) and Corynebacterium parvum.

Polyclonal antibodies are heterogeneous populations of antibodymolecules derived from the sera of animals immunized with an antigen,such as target gene product, or an antigenic functional derivativethereof. For the production of polyclonal antibodies, host animals suchas those described above, may be immunized by injection withdifferentially expressed or pathway gene product supplemented withadjuvants as also described above.

Monoclonal antibodies, which are homogeneous populations of antibodiesto a particular antigen, may be obtained by any technique which providesfor the production of antibody molecules by continuous cell lines inculture. These include, but are not limited to the hybridoma techniqueof Kohler and Milstein, (1975, Nature 256:495-497; and U.S. Pat. No.4,376,110), the human B-cell hybridoma technique (Kosbor et al., 1983,Immunology Today 4:72; Cole et al., 1983, Proc. Natl. Acad. Sci. USA80:2026-2030), and the EBV-hybridoma technique (Cole et al., 1985,Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp.77-96). Such antibodies may be of any immunoglobulin class includingIgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridomaproducing the mAb of this invention may be cultivated in vitro or invivo. Production of high titers of mAbs in vivo makes this the presentlypreferred method of production.

In addition, techniques developed for the production of “chimericantibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci.,81:6851-6855; Neuberger et al., 1984, Nature, 312:604-608; Takeda etal., 1985, Nature, 314:452-454) by splicing the genes from a mouseantibody molecule of appropriate antigen specificity together with genesfrom a human antibody molecule of appropriate biological activity can beused. A chimeric antibody is a molecule in which different portions arederived from different animal species, such as those having a variableregion derived from a murine mAb and a human immunoglobulin constantregion.

Alternatively, techniques described for the production of single chainantibodies (U.S. Pat. No. 4,946,778; Bird, 1988, Science 242:423-426;Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; and Wardet al., 1989, Nature 334:544-546) can be adapted to producedifferentially expressed or pathway gene-single chain antibodies. Singlechain antibodies are formed by linking the heavy and light chainfragments of the Fv region via an amino acid bridge, resulting in asingle chain polypeptide.

Antibody fragments which recognize specific epitopes may be generated byknown techniques. For example, such fragments include but are notlimited to: the F(ab′)₂ fragments which can be produced by pepsindigestion of the antibody molecule and the Fab fragments which can begenerated by reducing the disulfide bridges of the F(ab′)₂ fragments.Alternatively, Fab expression libraries may be constructed (Huse et al.,1989, Science, 246:1275-1281) to allow rapid and easy identification ofmonoclonal Fab fragments with the desired specificity.

5.4.4. CELL- AND ANIMAL-BASED MODEL SYSTEMS

Described herein are cell- and animal-based systems which act as modelsfor cardiovascular disease. These systems may be used in a variety ofapplications. For example, the cell- and animal-based model systems maybe used to further characterize differentially expressed and pathwaygenes, as described, above, in Section 5.3. Such furthercharacterization may, for example, indicate that a differentiallyexpressed gene is a target gene. Second, such assays may be utilized aspart of screening strategies designed to identify compounds which arecapable of ameliorating cardiovascular disease symptoms, as described,below, in Section 5.5.4. Thus, the animal- and cell-based models may beused to identify drugs, pharmaceuticals, therapies and interventionswhich may be effective in treating cardiovascular disease. In addition,as described in detail, below, in Section 5.7.1, such animal models maybe used to determine the LD₅₀ and the ED50 in animal subjects, and suchdata can be used to determine the in vivo efficacy of potentialcardiovascular disease treatments.

5.4.4.1. ANIMAL-BASED SYSTEMS

Animal-based model systems of cardiovascular disease may include, butare not limited to, non-recombinant and engineered transgenic animals.

Non-recombinant animal models for cardiovascular disease may include,for example, genetic models. Such genetic cardiovascular disease modelsmay include, for example, apoB or apoR deficient pigs (Rapacz, et al.,1986, Science 234:1573-1577) and Watanabe heritable hyperlipidemic(WHHL) rabbits (Kita et al., 1987, Proc. Natl. Acad. Sci USA 84:5928-5931).

Non-recombinant, non-genetic animal models of atherosclerosis mayinclude, for example, pig, rabbit, or rat models in which the animal hasbeen exposed to either chemical wounding through dietary supplementationof LDL, or mechanical wounding through balloon catheter angioplasty, forexample.

Additionally, animal models exhibiting cardiovascular disease symptomsmay be engineered by utilizing, for example, target gene sequences suchas those described, above, in Section 5.4.1, in conjunction withtechniques for producing transgenic animals that are well known to thoseof skill in the art. For example, target gene sequences may beintroduced into, and overexpressed in, the genome of the animal ofinterest, or, if endogenous target gene sequences are present, they mayeither be overexpressed or, alternatively, be disrupted in order tounderexpress or inactivate target gene expression, such as described forthe disruption of apoE in mice (Plump et al., 1992, Cell 71: 343-353).

In order to overexpress a target gene sequence, the coding portion ofthe target gene sequence may be ligated to a regulatory sequence whichis capable of driving gene expression in the animal and cell type ofinterest. Such regulatory regions will be well known to those of skillin the art, and may be utilized in the absence of undue experimentation.

The use of such a genetically engineered animal-based system isdescribed in detail in the example provided in Section 7, below, for thetarget gene bcl-2 (see Table 1, in Section 5.4.1, above). Briefly, bcl-2expression first was shown to be down-regulated in the apoE-deficientatherosclerosis mouse model. Then, a transgenic mouse was engineeredbearing the human bcl-2 gene under the control of a promoter which isinduced under atherogenic conditions. To test the effect of theinduction of bcl-2 under such conditions, the transgenic mouse iscrossed with the apoE-deficient mouse. apoE-deficient progeny bearingthe highly expressible bcl-2 gene are then examined for plaque formationand development. Reduction in plaque formation and development in theseprogeny confirms the effectiveness of intervening in cardiovasculardisease through this target gene.

For underexpression of an endogenous target gene sequence, such asequence may be isolated and engineered such that when reintroduced intothe genome of the animal of interest, the endogenous target gene alleleswill be inactivated. Preferably, the engineered target gene sequence isintroduced via gene targeting such that the endogenous target sequenceis disrupted upon integration of the engineered target gene sequenceinto the animal's genome. Gene targeting is discussed, below, in thisSection.

Animals of any species, including, but not limited to, mice, rats,rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates,e.g., baboons, monkeys, and chimpanzees may be used to generatecardiovascular disease animal models.

Any technique known in the art may be used to introduce a target genetransgene into animals to produce the founder lines of transgenicanimals. Such techniques include, but are not limited to pronuclearmicroinjection (Hoppe, P. C. and Wagner, T. E., 1989, U.S. Pat. No.4,873,191); retrovirus mediated gene transfer into germ lines (Van derPutten et al., 1985, Proc. Natl. Acad. Sci., USA 82:6148-6152); genetargeting in embryonic stem cells (Thompson et al., 1989, Cell56:313-321); electroporation of embryos (Lo, 1983, Mol Cell. Biol.3:1803-1814); and sperm-mediated gene transfer (Lavitrano et al., 1989,Cell 57:717-723); etc. For a review of such techniques, see Gordon,1989, Transgenic Animals, Intl. Rev. Cytol. 115:171-229, which isincorporated by reference herein in its entirety.

The present invention provides for transgenic animals that carry thetransgene in all their cells, as well as animals which carry thetransgene in some, but not all their cells, i.e., mosaic animals. Thetransgene may be integrated as a single transgene or in concatamers,e.g., head-to-head tandems or head-to-tail tandems. The transgene mayalso be selectively introduced into and activated in a particular celltype by following, for example, the teaching of Lasko et al. (Lasko, M.et al., 1992, Proc. Natl. Acad. Sci. USA 89: 6232-6236). The regulatorysequences required for such a cell-type specific activation will dependupon the particular cell type of interest, and will be apparent to thoseof skill in the art. When it is desired that the target gene transgenebe integrated into the chromosomal site of the endogenous target gene,gene targeting is preferred. Briefly, when such a technique is to beutilized, vectors containing some nucleotide sequences homologous to theendogenous target gene of interest are designed for the purpose ofintegrating, via homologous recombination with chromosomal sequences,into and disrupting the function of the nucleotide sequence of theendogenous target gene. The transgene may also be selectively introducedinto a particular cell type, thus inactivating the endogenous gene ofinterest in only that cell type, by following, for example, the teachingof Gu et al. (Gu, et al., 1994, Science 265: 103-106). The regulatorysequences required for such a cell-type specific inactivation willdepend upon the particular cell type of interest, and will be apparentto those of skill in the art.

Once transgenic animals have been generated, the expression of therecombinant target gene and protein may be assayed utilizing standardtechniques. Initial screening may be accomplished by Southern blotanalysis or PCR techniques to analyze animal tissues to assay whetherintegration of the transgene has taken place. The level of mRNAexpression of the transgene in the tissues of the transgenic animals mayalso be assessed using techniques which include but are not limited toNorthern blot analysis of tissue samples obtained from the animal, insitu hybridization analysis, and RT-PCR. Samples of targetgene-expressing tissue, may also be evaluated immunocytochemically usingantibodies specific for the target gene transgene gene product ofinterest.

The target gene transgenic animals that express target gene mRNA ortarget gene transgene peptide (detected immunocytochemically, usingantibodies directed against the target gene product's epitopes) ateasily detectable levels should then be further evaluated to identifythose animals which display characteristic cardiovascular diseasesymptoms. Such symptoms may include, for example, increased prevalenceand size of fatty streaks and/or cardiovascular disease plaques.

Additionally, specific cell types within the transgenic animals may beanalyzed and assayed for cellular phenotypes characteristic ofcardiovascular disease. In the case of monocytes, such phenotypes mayinclude but are not limited to increases in rates of LDL uptake,adhesion to endothelial cells, transmigration, foam cell formation,fatty streak formation, and production of foam cell specific products.Cellular phenotype assays are discussed in detail in Section 5.4.4.2,below. Further, such cellular phenotypes may include a particular celltype's fingerprint pattern of expression as compared to knownfingerprint expression profiles of the particular cell type in animalsexhibiting cardiovascular disease symptoms. Fingerprint profiles aredescribed in detail in Section 5.8.1, below. Such transgenic animalsserve as suitable model systems for cardiovascular disease.

Once target gene transgenic founder animals are produced, they may bebred, inbred, outbred, or crossbred to produce colonies of theparticular animal. Examples of such breeding strategies include but arenot limited to: outbreeding of founder animals with more than oneintegration site in order to establish separate lines; inbreeding ofseparate lines in order to produce compound target gene transgenics thatexpress the target gene transgene of interest at higher levels becauseof the effects of additive expression of each target gene transgene;crossings of heterozygous transgenic animals to produce animalshomozygous for a given integration site in order both to augmentexpression and eliminate the possible need for screening of animals byDNA analysis; crossing of separate homozygous lines to produce compoundheterozygous or homozygous lines; breeding animals to different inbredgenetic backgrounds so as to examine effects of modifying alleles onexpression of the target gene transgene and the development ofcardiovascular disease symptoms. One such approach is to cross thetarget gene transgenic founder animals with a wild type strain toproduce an F1 generation that exhibits cardiovascular disease symptoms.The F1 generation may then be inbred in order to develop a homozygousline, if it is found that homozygous target gene transgenic animals areviable.

5.4.4.2. CELL-BASED ASSAYS

Cells that contain and express target gene sequences which encode targetgene protein, and, further, exhibit cellular phenotypes associated withcardiovascular disease, may be utilized to identify compounds thatexhibit anti-cardiovascular disease activity. In the case of monocytes,such phenotypes may include but are not limited to increases in rates ofLDL uptake, adhesion to endothelial cells, transmigration, foam cellformation, fatty streak formation, and production by foam cells ofgrowth factors such as bFGF, IGF-I, VEGF, IL-1, M-CSF, TGFβ, TGFα, TNFα,HB-EGF, PDGF, IFN-γ and GM-CSF. Transmigration rates, for example, maybe measured using the in vitro system of Navab et al., described inSection 5.1.1.3, above, by quantifying the number of monocytes thatmigrate across the endothelial monolayer and into the collagen layer ofthe subendothelial space.

Such cells may include non-recombinant cell lines, such as U937 (ATCC#CRL1593) and THP-1 (TIB202). Further, such cells may includerecombinant, transgenic cell lines. For example, the cardiovasculardisease animal models of the invention, discussed, above, in Section5.4.4.1, may be used to generate cell lines, containing one or more celltypes involved in cardiovascular disease, that can be used as cellculture models for this disorder. While primary cultures derived fromthe cardiovascular disease transgenic animals of the invention may beutilized, the generation of continuous cell lines is preferred. Forexamples of techniques which may be used to derive a continuous cellline from the transgenic animals, see Small et al., 1985, Mol. CellBiol. 5:642-648.

Alternatively, cells of a cell type known to be involved incardiovascular disease may be transfected with sequences capable ofincreasing or decreasing the amount of target gene expression within thecell. For example, target gene sequences may be introduced into, andoverexpressed in, the genome of the cell of interest, or, if endogenoustarget gene sequences are present, they may be either overexpressed or,alternatively disrupted in order to underexpress or inactivate targetgene expression.

In order to overexpress a target gene sequence, the coding portion ofthe target gene sequence may be ligated to a regulatory sequence whichis capable of driving gene expression in the cell type of interest. Suchregulatory regions will be well known to those of skill in the art, andmay be utilized in the absence of undue experimentation.

For underexpression of an endogenous target gene sequence, such asequence may be isolated and engineered such that when reintroduced intothe genome of the cell type of interest, the endogenous target genealleles will be inactivated. Preferably, the engineered target genesequence is introduced via gene targeting such that the endogenoustarget sequence is disrupted upon integration of the engineered targetgene sequence into the cell's genome. Target gene introduction isdiscussed, above, in Section 5.4.4.1.

Transfection of target gene sequence nucleic acid may be accomplished byutilizing standard techniques. See, for example, Ausubel, 1989, supra.Transfected cells should be evaluated for the presence of therecombinant target gene sequences, for expression and accumulation oftarget gene mRNA, and for the presence of recombinant target geneprotein production. In instances wherein a decrease in target geneexpression is desired, standard techniques may be used to demonstratewhether a decrease in endogenous target gene expression and/or in targetgene product production is achieved.

5.5. SCREENING ASSAYS FOR COMPOUNDS THAT INTERACT WITH THE TARGET GENEPRODUCT

The following assays are designed to identify compounds that bind totarget gene products, bind to other cellular or extracellular proteinsthat interact with a target gene product, and interfere with theinteraction of the target gene product with other cellular orextracellular proteins. For example, in the case of the rchd523 geneproduct, which is a transmembrane receptor-type protein, such techniquescan identify ligands for such a receptor. An rchd523 gene product ligandcan, for example, act as the basis for amelioration of suchcardiovascular diseases as atherosclerosis, ischemia/reperfusion,hypertension, restenosis, and arterial inflammation, given that rchd523up-regulation is specific to endothelial cells. Such compounds mayinclude, but are not limited to peptides, antibodies, or small organicor inorganic compounds. Methods for the identification of such compoundsare described in Section 5.5.1, below. Such compounds may also includeother cellular proteins. Methods for the identification of such cellularproteins are described, below, in Section 5.5.2.

Compounds identified via assays such as those described herein may beuseful, for example, in elaborating the biological function of thetarget gene product, and for ameliorating cardiovascular disease. Ininstances whereby a cardiovascular disease condition results from anoverall lower level of target gene expression and/or target gene productin a cell or tissue, compounds that interact with the target geneproduct may include compounds which accentuate or amplify the activityof the bound target gene protein. Such compounds would bring about aneffective increase in the level of target gene product activity, thusameliorating symptoms.

In other instances mutations within the target gene may cause aberranttypes or excessive amounts of target gene proteins to be made which havea deleterious effect that leads to cardiovascular disease. Similarly,physiological conditions may cause an excessive increase in target geneexpression leading to cardiovascular disease. In such cases, compoundsthat bind target gene protein may be identified that inhibit theactivity of the bound target gene protein. Assays for testing theeffectiveness of compounds, identified by, for example, techniques suchas those described in this Section are discussed, below, in Section5.5.4.

5.5.1. IN VITRO SCREENING ASSAYS FOR COMPOUNDS THAT BIND TO THE TARGETGENE PRODUCT

In vitro systems may be designed to identify compounds capable ofbinding the target gene of the invention. Such compounds may include,but are not limited to, peptides made of D-and/or L-configuration aminoacids (in, for example, the form of random peptide libraries; see e.g.,Lam, K. S. et al., 1991, Nature 354:82-84), phosphopeptides (in, forexample, the form of random or partially degenerate, directedphosphopeptide libraries; see, e.g., Songyang, Z. et al., 1993, Cell72:767-778), antibodies, and small organic or inorganic molecules.Compounds identified may be useful, for example, in modulating theactivity of target gene proteins, preferably mutant target geneproteins, may be useful in elaborating the biological function of thetarget gene protein, may be utilized in screens for identifyingcompounds that disrupt normal target gene interactions, or may inthemselves disrupt such interactions.

The principle of the assays used to identify compounds that bind to thetarget gene protein involves preparing a reaction mixture of the targetgene protein and the test compound under conditions and for a timesufficient to allow the two components to interact and bind, thusforming a complex which can be removed and/or detected in the reactionmixture. These assays can be conducted in a variety of ways. Forexample, one method to conduct such an assay would involve anchoring thetarget gene or the test substance onto a solid phase and detectingtarget gene/test substance complexes anchored on the solid phase at theend of the reaction. In one embodiment of such a method, the target geneprotein may be anchored onto a solid surface, and the test compound,which is not anchored, may be labeled, either directly or indirectly.

In practice, microtitre plates are conveniently utilized. The anchoredcomponent may be immobilized by non-covalent or covalent attachments.Non-covalent attachment may be accomplished simply by coating the solidsurface with a solution of the protein and drying. Alternatively, animmobilized antibody, preferably a monoclonal antibody, specific for theprotein may be used to anchor the protein to the solid surface. Thesurfaces may be prepared in advance and stored.

In order to conduct the assay, the nonimmobilized component is added tothe coated surface containing the anchored component. After the reactionis complete, unreacted components are removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized on thesolid surface. The detection of complexes anchored on the solid surfacecan be accomplished in a number of ways. Where the previouslynonimmobilized component is pre-labeled, the detection of labelimmobilized on the surface indicates that complexes were formed. Wherethe previously nonimmobilized component is not pre-labeled, an indirectlabel can be used to detect complexes anchored on the surface; e.g.,using a labeled antibody specific for the previously nonimmobilizedcomponent (the antibody, in turn, may be directly labeled or indirectlylabeled with a labeled anti-Ig antibody).

Alternatively, a reaction can be conducted in a liquid phase, thereaction products separated from unreacted components, and complexesdetected; e.g., using an immobilized antibody specific for target geneproduct or the test compound to anchor any complexes formed in solution,and a labeled antibody specific for the other component of the possiblecomplex to detect anchored complexes.

Compounds that are shown to bind to a particular target gene productthrough one of the methods described above can be further tested fortheir ability to elicit a biochemical response from the target geneprotein. A particular embodiment is described herein for receptorproteins involved in signal transduction, including but not limited tothe rchd523 gene product. Compounds that interact with a target geneproduct receptor domain, can be screened for their ability to functionas ligands, i.e., to bind to the receptor protein in a manner thattriggers the signal transduction pathway. Useful receptor fragments oranalogs in the invention are those which interact with ligand. Thereceptor component can be assayed functionally, i.e., for its ability tobind ligand and mobilize Ca⁺⁺ (see below). These assays include, ascomponents, ligand and a recombinant target gene product (or a suitablefragment or analog) configured to permit detection of binding.

For example, and not by way of limitation, a recombinant receptor may beused to screen for ligands by its ability to mediate ligand-dependentmobilization of calcium. Cells, preferably myeloma cells or Xenopusoocytes, transfected with a target gene expression vector (constructedaccording to the methods described in Section 5.4.2, above) are loadedwith FURA-2 or INDO-1 by standard techniques. Mobilization of Ca²⁺induced by ligand is measured by fluorescence spectroscopy as previouslydescribed (Grynkiewicz et al., 1985, J. Biol. Chem. 260:3440). Ligandsthat react with the target gene product receptor domain, therefore, canbe identified by their ability to produce a fluorescent signal. Theirreceptor binding activities can be quantified and compared by measuringthe level of fluorescence produced over background.

The rchd523 gene product consists of a G protein-coupled receptor withmultiple transmembrane domains. The Ca²⁺ mobilization assay, therefore,can be used to screen compounds that are ligands of the rchd523receptor. This screening method is described in detail with respect torchd523 in the example in Section 12, below. Identification of rchd523ligand, and measuring the activity of the ligand-receptor complex, leadsto the identification of antagonists of this interaction, as describedin Section 5.5.3, below. Such antagonists are useful in the treatment ofcardiovascular disease.

30 5.5.2. ASSAYS FOR CELLULAR OR EXTRACELLULAR PROTEINS THAT INTERACTWITH THE TARGET GENE PRODUCT

Any method suitable for detecting protein-protein interactions may beemployed for identifying novel target protein-cellular or extracellularprotein interactions. These methods are outlined in Section 5.2., supra,for the identification of pathway genes, and may be utilized herein withrespect to the identification of proteins which interact with identifiedtarget proteins. In such a case, the target gene serves as the known“bait” gene.

5.5.3. ASSAYS FOR COMPOUNDS THAT INTERFERE WITH INTERACTION BETWEENTARGET GENE PRODUCT AND OTHER COMPOUNDS

The target gene proteins of the invention may, in vivo, interact withone or more cellular or extracellular proteins. Such proteins mayinclude, but are not limited to, those proteins identified via methodssuch as those described, above, in Section 5.5.2. For the purposes ofthis discussion, target gene products and such cellular andextracellular proteins are referred to herein as “binding partners”.Compounds that disrupt such interactions may be useful in regulating theactivity of the target gene proteins, especially mutant target geneproteins. Such compounds may include, but are not limited to moleculessuch as antibodies, peptides, and the like described in Section 5.5.1.above.

The basic principle of the assay systems used to identify compounds thatinterfere with the interaction between the target gene protein, and itscellular or extracellular protein binding partner or partners involvespreparing a reaction mixture containing the target gene protein and thebinding partner under conditions and for a time sufficient to allow thetwo proteins to interact and bind, thus forming a complex. In order totest a compound for inhibitory activity, the reaction mixture isprepared in the presence and absence of the test compound. The testcompound may be initially included in the reaction mixture or may beadded at a time subsequent to the addition of target gene and itscellular or extracellular binding partner. Control reaction mixtures areincubated without the test compound or with a placebo. The formation ofany complexes between the target gene protein and the cellular orextracellular binding partner is then detected. The formation of acomplex in the control reaction, but not in the reaction mixturecontaining the test compound, indicates that the compound interfereswith the interaction of the target gene protein and the interactivebinding partner protein. Additionally, complex formation within reactionmixtures containing the test compound and a normal target gene proteinmay also be compared to complex formation within reaction mixturescontaining the test compound and mutant target gene protein. Thiscomparison may be important in those cases wherein it is desirable toidentify compounds that disrupt interactions of mutant but not normaltarget gene proteins.

The assay for compounds that interfere with the interaction of thebinding partners can be conducted in a heterogeneous or homogeneousformat. Heterogeneous assays involve anchoring one of the bindingpartners onto a solid phase and detecting complexes anchored on thesolid phase at the end of the reaction. In homogeneous assays, theentire reaction is carried out in a liquid phase. In either approach,the order of addition of reactants can be varied to obtain differentinformation about the compounds being tested. For example, testcompounds that interfere with the interaction between the bindingpartners, e.g., by competition, can be identified by conducting thereaction in the presence of the test substance; i.e., by adding the testsubstance to the reaction mixture prior to or simultaneously with thetarget gene protein and interactive cellular or extracellular protein.Alternatively, test compounds that disrupt preformed complexes, e.g.compounds with higher binding constants that displace one of the bindingpartners from the complex, can be tested by adding the test compound tothe reaction mixture after complexes have been formed. The variousformats are described briefly below.

In a heterogeneous assay system, either the target gene protein or theinteractive cellular or extracellular binding partner protein, isanchored onto a solid surface, and its binding partner, which is notanchored, is labeled, either directly or indirectly. In practice,microtitre plates are conveniently utilized. The anchored species may beimmobilized by non-covalent or covalent attachments. Non-covalentattachment may be accomplished simply by coating the solid surface witha solution of the protein and drying. Alternatively, an immobilizedantibody specific for the protein may be used to anchor the protein tothe solid surface. The surfaces may be prepared in advance and stored.

In order to conduct the assay, the binding partner of the immobilizedspecies is exposed to the coated surface with or without the testcompound. After the reaction is complete, unreacted components areremoved (e.g., by washing) and any complexes formed will remainimmobilized on the solid surface. The detection of complexes anchored onthe solid surface can be accomplished in a number of ways. Where thebinding partner was pre-labeled, the detection of label immobilized onthe surface indicates that complexes were formed. Where the bindingpartner is not pre-labeled, an indirect label can be used to detectcomplexes anchored on the surface; e.g., using a labeled antibodyspecific for the binding partner (the antibody, in turn, may be directlylabeled or indirectly labeled with a labeled anti-Ig antibody).Depending upon the order of addition of reaction components, testcompounds which inhibit complex formation or which disrupt preformedcomplexes can be detected.

Alternatively, the reaction can be conducted in a liquid phase in thepresence or absence of the test compound, the reaction productsseparated from unreacted components, and complexes detected; e.g., usingan immobilized antibody specific for one binding partner to anchor anycomplexes formed in solution, and a labeled antibody specific for theother binding partner to detect anchored complexes. Again, dependingupon the order of addition of reactants to the liquid phase, testcompounds which inhibit complex or which disrupt preformed complexes canbe identified.

In an alternate embodiment of the invention, a homogeneous assay can beused. In this approach, a preformed complex of the target gene proteinand the interactive cellular or extracellular protein is prepared inwhich one of the binding partners is labeled, but the signal generatedby the label is quenched due to complex formation (see, e.g., U.S. Pat.No. 4,109,496 by Rubenstein which utilizes this approach forimmunoassays). The addition of a test substance that competes with anddisplaces one of the binding partners from the preformed complex willresult in the generation of a signal above background. In this way, testsubstances which disrupt target gene protein-cellular or extracellularprotein interaction can be identified.

In a particular embodiment, the target gene protein can be prepared forimmobilization using recombinant DNA techniques described in Section5.4.2, supra. For example, the target gene coding region can be fused toa glutathione-S-transferase (GST) gene, using a fusion vector such aspGEX-5X-1, in such a manner that its binding activity is maintained inthe resulting fusion protein. The interactive cellular or extracellularprotein can be purified and used to raise a monoclonal antibody, usingmethods routinely practiced in the art and described above, in Section5.4.3. This antibody can be labeled with the radioactive isotope ¹²⁵I,for example, by methods routinely practiced in the art. In aheterogeneous assay, e.g., the GST-target gene fusion protein can beanchored to glutathione-agarose beads. The interactive cellular orextracellular binding partner protein can then be added in the presenceor absence of the test compound in a manner that allows interaction andbinding to occur. At the end of the reaction period, unbound materialcan be washed away, and the labeled monoclonal antibody can be added tothe system and allowed to bind to the complexed binding partners. Theinteraction between the target gene protein and the interactive cellularor extracellular binding partner protein can be detected by measuringthe amount of radioactivity that remains associated with theglutathione-agarose beads. A successful inhibition of the interaction bythe test compound will result in a decrease in measured radioactivity.

Alternatively, the GST-target gene fusion protein and the interactivecellular or extracellular binding partner protein can be mixed togetherin liquid in the absence of the solid glutathione-agarose beads. Thetest compound can be added either during or after the binding partnersare allowed to interact. This mixture can then be added to theglutathione-agarose beads and unbound material is washed away. Again theextent of inhibition of the binding partner interaction can be detectedby adding the labeled antibody and measuring the radioactivityassociated with the beads.

In another embodiment of the invention, these same techniques can beemployed using peptide fragments that correspond to the binding domainsof the target gene protein and the interactive cellular or extracellularprotein, respectively, in place of one or both of the full lengthproteins. Any number of methods routinely practiced in the art can beused to identify and isolate the protein's binding site. These methodsinclude, but are not limited to, mutagenesis of one of the genesencoding the proteins and screening for disruption of binding in aco-immunoprecipitation assay. Compensating mutations in the target genecan be selected. Sequence analysis of the genes encoding the respectiveproteins will reveal the mutations that correspond to the region of theprotein involved in interactive binding. Alternatively, one protein canbe anchored to a solid surface using methods described in this Sectionabove, and allowed to interact with and bind to its labeled bindingpartner, which has been treated with a proteolytic enzyme, such astrypsin. After washing, a short, labeled peptide comprising the bindingdomain may remain associated with the solid material, which can beisolated and identified by amino acid sequencing. Also, once the genecoding for the for the cellular or extracellular protein is obtained,short gene segments can be engineered to express peptide fragments ofthe protein, which can then be tested for binding activity and purifiedor synthesized.

For example, and not by way of limitation, target gene can be anchoredto a solid material as described above in this Section by making aGST-target gene fusion protein and allowing it to bind to glutathioneagarose beads. The interactive cellular or extracellular binding partnerprotein can be labeled with a radioactive isotope, such as ³⁵S, andcleaved with a proteolytic enzyme such as trypsin. Cleavage products canthen be added to the anchored GST-target gene fusion protein and allowedto bind. After washing away unbound peptides, labeled bound material,representing the cellular or extracellular binding partner proteinbinding domain, can be eluted, purified, and analyzed for amino acidsequence by techniques well known in the art; e.g., using the Edmandegradation procedure (see e.g., Creighton, 1983, Proteins: Structuresand Molecular Principles, W. H. Freeman & Co., New York, pp. 34-49).Peptides so identified can be produced, using techniques well known inthe art, either synthetically (see e.g., Creighton, 1983, supra at pp.50-60) or, if the gene has already been isolated, by using recombinantDNA technology, as described in Section 5.4.2, supra.

A particular embodiment of the invention features a method of screeningcandidate compounds for their ability to antagonize the interactionbetween ligand and the receptor domain of a target gene product,including but not limited to the receptor domain of the rchd523 geneproduct. The rchd523 gene product, which is a G protein-coupled receptorprotein containing multiple transmembrane domains, is especially usefulin screening for antagonists of ligand-receptor interactions. The methodinvolves: a) mixing a candidate antagonist compound with a firstcompound which includes a recombinant target gene product comprising areceptor domain (or ligand-binding fragment or analog) on the one handand with a second compound which includes ligand on the other hand; b)determining whether the first and second compounds bind; and c)identifying antagonistic compounds as those which interfere with thebinding of the first compound to the second compound and/or which reducethe ligand-mediated release of intracellular Ca⁺⁺.

By an “antagonist” is meant a molecule which inhibits a particularactivity, in this case, the ability of ligand to interact with a targetgene product receptor domain and/or to trigger the biological eventsresulting from such an interaction (e.g., release of intracellularCa⁺⁺). Preferred therapeutics include antagonists, e.g., peptidefragments (particularly, fragments derived from the N-terminalextracellular domain), antibodies (particularly, antibodies whichrecognize and bind the N-terminal extracellular domain), or drugs, whichblock ligand or target gene product function by interfering with theligand-receptor interaction.

Because the receptor component of the target gene product can beproduced by recombinant techniques and because candidate antagonists maybe screened in vitro, the instant invention provides a simple and rapidapproach to the identification of useful therapeutics.

Specific receptor fragments of interest include any portions of thetarget gene products that are capable of interaction with ligand, forexample, all or part of the N-terminal extracellular domain. Suchportions include the transmembrane segments and portions of the receptordeduced to be extracellular. Such fragments may be useful as antagonists(as described above), and are also useful as immunogens for producingantibodies which neutralize the activity of the target gene product invivo (e.g., by interfering with the interaction between the receptor andligand; see below). Extracellular regions may be identified bycomparison with related proteins of similar structure (e.g., othermembers of the G-protein-coupled receptor superfamily); useful regionsare those exhibiting homology to the extracellular domains ofwell-characterized members of the family.

Alternatively, from the primary amino acid sequence, the secondaryprotein structure and, therefore, the extracellular domain regions maybe deduced semi-empirically using a hydrophobicity/hydrophilicitycalculation such as the Chou-Fasman method (see, e.g., Chou and Fasman,Ann. Rev. Biochem. 47:251, 1978). Hydrophilic domains, particularly onessurrounded by hydrophobic stretches (e.g., transmembrane domains)present themselves as strong candidates for extracellular domains.Finally, extracellular domains may be identified experimentally usingstandard enzymatic digest analysis, e.g., tryptic digest analysis.

Candidate fragments (e.g., all or part of the transmembrane segments orany extracellular fragment) are tested for interaction with ligand bythe assays described herein (e.g., the assay described above). Suchfragments are also tested for their ability to antagonize theinteraction between ligand and its endogenous receptor using the assaysdescribed herein. Analogs of useful receptor fragments (as describedabove) may also be produced and tested for efficacy as screeningcomponents or antagonists (using the assays described herein); suchanalogs are also considered to be useful in the invention.

Of particular interest are receptor fragments encompassing theextracellular main-terminal domain (or a ligand binding fragmentthereof). Also of interest are the target gene product extracellularloops. Peptide fragments derived from these extracellular loops may alsobe used as antagonists, particularly if the loops cooperate with theamino-terminal domain to facilitate ligand binding. Alternatively, suchloops and extracellular N-terminal domain (as well as the full lengthtarget gene product) provide immunogens for producing anti-target geneproduct antibodies.

Binding of ligand to its receptor may be assayed by any of the methodsdescribed above in Section 5.5.1. Preferably, cells expressingrecombinant target gene product (or a suitable target gene productfragment or analog) are immobilized on a solid substrate (e.g., the wallof a microtitre plate or a column) and reacted with detectably-labelledligand (as described above). Binding is assayed by the detection labelin association with the receptor component (and, therefore, inassociation with the solid substrate). Binding of labelled ligand toreceptor-bearing cells is used as a “control” against which antagonistassays are measured. The antagonist assays involve incubation of thetarget gene product-bearing cells with an appropriate amount ofcandidate antagonist. To this mix, an equivalent amount to labelledligand is added. An antagonist useful in the invention specificallyinterferes with labelled ligand binding to the immobilizedreceptor-expressing cells.

An antagonist is then tested for its ability to interfere with ligandfunction, i.e., to specifically interfere with labelled ligand bindingwithout resulting in signal transduction normally mediated by thereceptor. To test this using a functional assay, stably transfected celllines containing the target gene product can be produced as describedherein and reporter compounds such as the calcium binding agent, FURA-2,loaded into the cytoplasm by standard techniques. Stimulation of theheterologous target gene product with ligand or another agonist leads tointracellular calcium release and the concomitant fluorescence of thecalcium-FURA-2 complex. This provides a convenient means for measuringagonist activity. Inclusion of potential antagonists along with ligandallows for the screening and identification of authentic receptorantagonists as those which effectively block ligand binding withoutproducing fluorescence (i.e., without causing the mobilization ofintracellular Ca⁺⁺). Such an antagonist may be expected to be a usefultherapeutic agent for cardiovascular disorders.

Appropriate candidate antagonists include target gene product fragments,particularly fragments containing a ligand-binding portion adjacent toor including one or more transmembrane segments or an extracellulardomain of the receptor (described above); such fragments wouldpreferably including five or more amino acids. Other candidateantagonists include analogs of ligand and other peptides as well asnon-peptide compounds and anti-target gene product antibodies designedor derived from analysis of the receptor.

This screening method is described in detail with respect to the rchd523gene in the example in Section 12, below. Because the rchd523 geneproduct is a G protein-coupled receptor, antagonists of the interactionbetween the rchd523 gene product and its natural ligand provideexcellent candidates for compounds effective in the treatment ofcardiovascular disease.

5.5.4. ASSAYS FOR AMELIORATION OF CARDIOVASCULAR DISEASE SYMPTOMS

Any of the binding compounds, including but not limited to compoundssuch as those identified in the foregoing assay systems, may be testedfor the ability to ameliorate cardiovascular disease symptoms.Cell-based and animal model-based assays for the identification ofcompounds exhibiting such an ability to ameliorate cardiovasculardisease symptoms are described below.

First, cell-based systems such as those described, above, in Section5.4.4.2., may be used to identify compounds which may act to amelioratecardiovascular disease symptoms. For example, such cell systems may beexposed to a compound, suspected of exhibiting an ability to amelioratecardiovascular disease symptoms, at a sufficient concentration and for atime sufficient to elicit such an amelioration of cardiovascular diseasesymptoms in the exposed cells. After exposure, the cells are examined todetermine whether one or more of the cardiovascular disease cellularphenotypes has been altered to resemble a more normal or more wild type,non-cardiovascular disease phenotype. For example, and not by way oflimitation, in the case of monocytes, such more normal phenotypes mayinclude but are not limited to decreased rates of LDL uptake, adhesionto endothelial cells, transmigration, foam cell formation, fatty streakformation, and production by foam cells of growth factors such as bFGF,IGF-I, VEGF, IL-1, M-CSF, TGFβ, TGFα, TNFα, HB-EGF, PDGF, IFN-γ, andGM-CSF. Transmigration rates, for example, may be measured using the invitro system of Navab et al., described in Section 5.1.1.3, above, byquantifying the number of monocytes that migrate across the endothelialmonolayer and into the collagen layer of the subendothelial space.

In addition, animal-based cardiovascular disease systems, such as thosedescribed, above, in Section 5.4.4.1, may be used to identify compoundscapable of ameliorating cardiovascular disease symptoms. Such animalmodels may be used as test substrates for the identification of drugs,pharmaceuticals, therapies, and interventions which may be effective intreating cardiovascular disease. For example, animal models may beexposed to a compound, suspected of exhibiting an ability to amelioratecardiovascular disease symptoms, at a sufficient concentration and for atime sufficient to elicit such an amelioration of cardiovascular diseasesymptoms in the exposed animals. The response of the animals to theexposure may be monitored by assessing the reversal of disordersassociated with cardiovascular disease, for example, by counting thenumber of atherosclerotic plaques and/or measuring their size before andafter treatment.

With regard to intervention, any treatments which reverse any aspect ofcardiovascular disease symptoms should be considered as candidates forhuman cardiovascular disease therapeutic intervention. Dosages of testagents may be determined by deriving dose-response curves, as discussedin Section 5.7.1, below.

Additionally, gene expression patterns may be utilized to assess theability of a compound to ameliorate cardiovascular disease symptoms. Forexample, the expression pattern of one or more fingerprint genes mayform part of a “fingerprint profile” which may be then be used in suchan assessment. “Fingerprint profile”, as used herein, refers to thepattern of mRNA expression obtained for a given tissue or cell typeunder a given set of conditions. Such conditions may include, but arenot limited to, atherosclerosis, ischemia/reperfusion, hypertension,restenosis, and arterial inflammation, including any of the control orexperimental conditions described in the paradigms of Section 5.1.1,above. Fingerprint profiles may be generated, for example, by utilizinga differential display procedure, as discussed, above, in Section 5.1.2,Northern analysis and/or RT-PCR. Any of the gene sequences described,above, in Section 5.4.1. may be used as probes and/or PCR primers forthe generation and corroboration of such fingerprint profiles.

Fingerprint profiles may be characterized for known states, eithercardiovascular disease or normal, within the cell- and/or animal-basedmodel systems. Subsequently, these known fingerprint profiles may becompared to ascertain the effect a test compound has to modify suchfingerprint profiles, and to cause the profile to more closely resemblethat of a more desirable fingerprint.

For example, administration of a compound may cause the fingerprintprofile of a cardiovascular disease model system to more closelyresemble the control system. Administration of a compound may,alternatively, cause the fingerprint profile of a control system tobegin to mimic a cardiovascular disease state. Such a compound may, forexample, be used in further characterizing the compound of interest, ormay be used in the generation of additional animal models.

5.5.5. MONITORING OF EFFECTS DURING CLINICAL TRIALS

Monitoring the influence of compounds on cardiovascular disease statesmay be applied not only in basic drug screening, but also in clinicaltrials. In such clinical trials, the expression of a panel of genes thathave been discovered in one of the paradigms described in Section5.1.1.1 through 5.1.1.6 may be used as a “read out” of a particulardrug's effect on a cardiovascular disease state.

For example, and not by way of limitation, Paradigm A provides for theidentification of fingerprint genes that are up-regulated in monocytestreated with oxidized LDL. Thus, to study the effect of anti-oxidantdrugs, for example, in a clinical trial, blood may be drawn frompatients before and at different stages during treatment with such adrug. Their monocytes may then be isolated and RNA prepared and analyzedby differential display as described in Sections 6.1.1 and 6.1.2. Thelevels of expression of these fingerprint genes may be quantified byNorthern blot analysis or RT-PCR, as described in Section 6.1.2, or byone of the methods described in Section 5.8.1, or alternatively bymeasuring the amount of protein produced, by one of the methodsdescribed in Section 5.8.2. In this way, the fingerprint profiles mayserve as surrogate markers indicative of the physiological response ofmonocytes that have taken up oxidized LDL. Accordingly, this responsestate may be determined before, and at various points during, drugtreatment. This method is described in further detail in the example inSection 10, below.

This method may also be applied to the other paradigms disclosed herein.For example, and not by way of limitation, the fingerprint profile ofParadigm B reveals that bcl-2 and glutathione peroxidase are bothdown-regulated in the monocytes of patients exposed to a high lipiddiet, e.g. cholesterol or fat, that leads to high serum LDL levels.Drugs may be tested, for example, for their ability to ameliorate theeffects of hypercholesterolemia in clinical trials. Patients with highLDL levels may have their monocytes isolated before, and at differentstages after, drug treatment. The drug's efficacy may be measured bydetermining the degree of restored expression of bcl-2 and glutathioneperoxidase, as described above for the Paradigm A fingerprint profile.

5.6. COMPOUNDS AND METHODS FOR TREATMENT OF CARDIOVASCULAR DISEASE

Described below are methods and compositions whereby cardiovasculardisease symptoms may be ameliorated. Certain cardiovascular diseases arebrought about, at least in part, by an excessive level of gene product,or by the presence of a gene product exhibiting an abnormal or excessiveactivity. As such, the reduction in the level and/or activity of suchgene products would bring about the amelioration of cardiovasculardisease symptoms. Techniques for the reduction of target gene expressionlevels or target gene product activity levels are discussed in Section5.6.1, below.

Alternatively, certain other cardiovascular diseases are brought about,at least in part, by the absence or reduction of the level of geneexpression, or a reduction in the level of a gene product's activity. Assuch, an increase in the level of gene expression and/or the activity ofsuch gene products would bring about the amelioration of cardiovasculardisease symptoms. Techniques for increasing target gene expressionlevels or target gene product activity levels are discussed in Section5.6.2, below.

5.6.1. COMPOUNDS THAT INHIBIT EXPRESSION, SYNTHESIS OR ACTIVITY OFMUTANT TARGET GENE ACTIVITY

As discussed above, target genes involved in cardiovascular diseasedisorders can cause such disorders via an increased level of target geneactivity. As summarized in Table 1, above, and detailed in the examplesin Sections 8 and 9, below, a number of genes are now known to beup-regulated in endothelial cells under disease conditions.Specifically, rchd005, rchd024, rchd032, and rchd036 are allup-regulated in endothelial cells treated with IL-1. Furthermore,rchd502, rchd523, rchd528, rchd534, and endoperoxide synthase are allup-regulated in endothelial cells subjected to shear stress. A varietyof techniques may be utilized to inhibit the expression, synthesis, oractivity of such target genes and/or proteins.

For example, compounds such as those identified through assaysdescribed, above, in Section 5.5, which exhibit inhibitory activity, maybe used in accordance with the invention to ameliorate cardiovasculardisease symptoms. As discussed in Section 5.5, above, such molecules mayinclude, but are not limited to small organic molecules, peptides,antibodies, and the like. Inhibitory antibody techniques are described,below, in Section 5.6.1.2.

For example, compounds can be administered that compete with endogenousligand for the rchd523 gene product. The resulting reduction in theamount of ligand-bound rchd523 gene transmembrane protein will modulatedendothelial cell physiology. Compounds that can be particularly usefulfor this purpose include, for example, soluble proteins or peptides,such as peptides comprising one or more of the extracellular domains, orportions and/or analogs thereof, of the rchd523 gene product, including,for example, soluble fusion proteins such as Ig-tailed fusion proteins.(For a discussion of the production of Ig-tailed fusion proteins, see,for example, U.S. Pat. No. 5,116,964.). Alternatively, compounds, suchas ligand analogs or antibodies, that bind to the rchd523 gene productreceptor site, but do not activate the protein, (e.g., receptor-ligandantagonists) can be effective in inhibiting rchd523 gene productactivity.

Further, antisense and ribozyme molecules which inhibit expression ofthe target gene may also be used in accordance with the invention toinhibit the aberrant target gene activity. Such techniques aredescribed, below, in Section 5.6.1.1. Still further, also as described,below, in Section 5.6.1.1, triple helix molecules may be utilized ininhibiting the aberrant target gene activity.

5.6.1.1. INHIBITORY ANTISENSE, RIBOZYME AND TRIPLE HELIX APPROACHES

Among the compounds which may exhibit the ability to amelioratecardiovascular disease symptoms are antisense, ribozyme, and triplehelix molecules. Such molecules may be designed to reduce or inhibitmutant target gene activity. Techniques for the production and use ofsuch molecules are well known to those of skill in the art.

Anti-sense RNA and DNA molecules act to directly block the translationof mRNA by hybridizing to targeted mRNA and preventing proteintranslation. With respect to antisense DNA, oligodeoxyribonucleotidesderived from the translation initiation site, e.g., between the −10 and+10 regions of the target gene nucleotide sequence of interest, arepreferred.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specificcleavage of RNA. The mechanism of ribozyme action involves sequencespecific hybridization of the ribozyme molecule to complementary targetRNA, followed by an endonucleolytic cleavage. The composition ofribozyme molecules must include one or more sequences complementary tothe target gene mRNA, and must include the well known catalytic sequenceresponsible for mRNA cleavage. For this sequence, see U.S. Pat. No.5,093,246, which is incorporated by reference herein in its entirety. Assuch within the scope of the invention are engineered hammerhead motifribozyme molecules that specifically and efficiently catalyzeendonucleolytic cleavage of RNA sequences encoding target gene proteins.

Specific ribozyme cleavage sites within any potential RNA target areinitially identified by scanning the molecule of interest for ribozymecleavage sites which include the following sequences, GUA, GUU and GUC.Once identified, short RNA sequences of between 15 and 20ribonucleotides corresponding to the region of the target genecontaining the cleavage site may be evaluated for predicted structuralfeatures, such as secondary structure, that may render theoligonucleotide sequence unsuitable. The suitability of candidatesequences may also be evaluated by testing their accessibility tohybridization with complementary oligonucleotides, using ribonucleaseprotection assays.

Nucleic acid molecules to be used in triple helix formation for theinhibition of transcription should be single stranded and composed ofdeoxyribonucleotides. The base composition of these oligonucleotidesmust be designed to promote triple helix formation via Hoogsteen basepairing rules, which generally require sizeable stretches of eitherpurines or pyrimidines to be present on one strand of a duplex.Nucleotide sequences may be pyrimidine-based, which will result in TATand CGC⁺ triplets across the three associated strands of the resultingtriple helix. The pyrimidine-rich molecules provide base complementarityto a purine-rich region of a single strand of the duplex in a parallelorientation to that strand. In addition, nucleic acid molecules may bechosen that are purine-rich, for example, containing a stretch of Gresidues. These molecules will form a triple helix with a DNA duplexthat is rich in GC paris, in which the majority of the purine residuesare located on a single strand of the targeted duplex, resulting in GGCtriplets across the three strands in the triplex.

Alternatively, the potential sequences that can be targeted for triplehelix formation may be increased by creating a so called “switchback”nucleic acid molecule. Switchback molecules are synthesized in analternating 5′-3′, 3′-5′ manner, such that they base pair with first onestrand of a duplex and then the other, eliminating the necessity for asizeable stretch of either purines or pyrimidines to be present on onestrand of a duplex.

It is possible that the antisense, ribozyme, and/or triple helixmolecules described herein may reduce or inhibit the transcription(triple helix) and/or translation (antisense, ribozyme) of mRNA producedby both normal and mutant target gene alleles. In order to ensure thatsubstantially normal levels of target gene activity are maintained,nucleic acid molecules that encode and express target gene polypeptidesexhibiting normal activity may be introduced into cells via gene therapymethods such as those described, below, in Section 5.7. that do notcontain sequences susceptible to whatever antisense, ribozyme, or triplehelix treatments are being utilized. Alternatively, it may be preferableto coadminister normal target gene protein into the cell or tissue inorder to maintain the requisite level of cellular or tissue target geneactivity.

Anti-sense RNA and DNA, ribozyme, and triple helix molecules of theinvention may be prepared by any method known in the art for thesynthesis of DNA and RNA molecules. These include techniques forchemically synthesizing oligodeoxyribonucleotides andoligoribonucleotides well known in the art such as for example solidphase phosphoramidite chemical synthesis. Alternatively, RNA moleculesmay be generated by in vitro and in vivo transcription of DNA sequencesencoding the antisense RNA molecule. Such DNA sequences may beincorporated into a wide variety of vectors which incorporate suitableRNA polymerase promoters such as the T7 or SP6 polymerase promoters.Alternatively, antisense cDNA constructs that synthesize antisense RNAconstitutively or inducibly, depending on the promoter used, can beintroduced stably into cell lines.

Various well-known modifications to the DNA molecules may be introducedas a means of increasing intracellular stability and half-life. Possiblemodifications include but are not limited to the addition of flankingsequences of ribonucleotides or deoxyribonucleotides to the 5′ and/or 3′ends of the molecule or the use of phosphorothioate or 2′ O-methylrather than phosphodiesterase linkages within theoligodeoxyribonucleotide backbone.

5.6.1.2. ANTIBODIES FOR TARGET GENE PRODUCTS

Antibodies that are both specific for target gene protein and interferewith its activity may be used to inhibit target gene function. Suchantibodies may be generated using standard techniques described inSection 5.4.3., supra, against the proteins themselves or againstpeptides corresponding to portions of the proteins. Such antibodiesinclude but are not limited to polyclonal, monoclonal, Fab fragments,single chain antibodies, chimeric antibodies, etc.

In instances where the target gene protein is intracellular and wholeantibodies are used, internalizing antibodies may be preferred. However,lipofectin liposomes may be used to deliver the antibody or a fragmentof the Fab region which binds to the target gene epitope into cells.Where fragments of the antibody are used, the smallest inhibitoryfragment which binds to the target protein's binding domain ispreferred. For example, peptides having an amino acid sequencecorresponding to the domain of the variable region of the antibody thatbinds to the target gene protein may be used. Such peptides may besynthesized chemically or produced via recombinant DNA technology usingmethods well known in the art (e.g., see Creighton, 1983, supra; andSambrook et al., 1989, supra). Alternatively, single chain neutralizingantibodies which bind to intracellular target gene epitopes may also beadministered. Such single chain antibodies may be administered, forexample, by expressing nucleotide sequences encoding single-chainantibodies within the target cell population by utilizing, for example,techniques such as those described in Marasco et al. (Marasco, W. etal., 1993, Proc. Natl. Acad. Sci. USA 90:7889-7893).

In some instances, the target gene protein is extracellular, or is atransmembrane protein, such as the rchd523 gene product. Antibodies thatare specific for one or more extracellular domains of the rchd523 geneproduct, for example, and that interfere with its activity, areparticularly useful in treating cardiovascular disease. Such antibodiesare especially efficient because they can access the target domainsdirectly from the bloodstream. Any of the administration techniquesdescribed, below in Section 5.7 which are appropriate for peptideadministration may be utilized to effectively administer inhibitorytarget gene antibodies to their site of action.

5.6.2. METHODS FOR RESTORING TARGET GENE ACTIVITY

Target genes that cause cardiovascular disease may be underexpressedwithin cardiovascular disease situations. As summarized in Table 1,above, and detailed in the example in Sections 7, below, several genesare now known to be down-regulated in monocytes under diseaseconditions. Specifically, bcl-2 and glutathione peroxidase geneexpression is down-regulated in the monocytes of patients exposed to ahigh lipid diet, e.g. cholesterol or fat, that leads to high serum LDLlevels. Alternatively, the activity of target gene products may bediminished, leading to the development of cardiovascular diseasesymptoms. Described in this Section are methods whereby the level oftarget gene activity may be increased to levels wherein cardiovasculardisease symptoms are ameliorated. The level of gene activity may beincreased, for example, by either increasing the level of target geneproduct present or by increasing the level of active target gene productwhich is present.

For example, a target gene protein, at a level sufficient to amelioratecardiovascular disease symptoms may be administered to a patientexhibiting such symptoms. Any of the techniques discussed, below, inSection 5.7, may be utilized for such administration. One of skill inthe art will readily know how to determine the concentration ofeffective, non-toxic doses of the normal target gene protein, utilizingtechniques such as those described, below, in Section 5.7.1.

Additionally, RNA sequences encoding target gene protein may be directlyadministered to a patient exhibiting cardiovascular disease symptoms, ata concentration sufficient to produce a level of target gene proteinsuch that cardiovascular disease symptoms are ameliorated. Any of thetechniques discussed, below, in Section 5.7, which achieve intracellularadministration of compounds, such as, for example, liposomeadministration, may be utilized for the administration of such RNAmolecules. The RNA molecules may be produced, for example, byrecombinant techniques such as those described, above, in Section 5.4.2.

Further, patients may be treated by gene replacement therapy. One ormore copies of a normal target gene, or a portion of the gene thatdirects the production of a normal target gene protein with target genefunction, may be inserted into cells using vectors which include, butare not limited to adenovirus, adeno-associated virus, and retrovirusvectors, in addition to other particles that introduce DNA into cells,such as liposomes. Additionally, techniques such as those describedabove may be utilized for the introduction of normal target genesequences into human cells.

Cells, preferably, autologous cells, containing normal target geneexpressing gene sequences may then be introduced or reintroduced intothe patient at positions which allow for the amelioration ofcardiovascular disease symptoms. Such cell replacement techniques may bepreferred, for example, when the target gene product is a secreted,extracellular gene product.

5.7. PHARMACEUTICAL PREPARATIONS AND METHODS OF ADMINISTRATION

The identified compounds that inhibit target gene expression, synthesisand/or activity can be administered to a patient at therapeuticallyeffective doses to treat or ameliorate cardiovascular disease. Atherapeutically effective dose refers to that amount of the compoundsufficient to result in amelioration of symptoms of cardiovasculardisease.

5.7.1. EFFECTIVE DOSE

Toxicity and therapeutic efficacy of such compounds can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD₅₀ (the dose lethal to 50% of thepopulation) and the ED₅₀ (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD₅₀/ED₅₀.Compounds which exhibit large therapeutic indices are preferred. Whilecompounds that exhibit toxic side effects may be used, care should betaken to design a delivery system that targets such compounds to thesite of affected tissue in order to minimize potential damage touninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED₅₀ with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the method of the invention, the therapeutically effective dose canbe estimated initially from cell culture assays. A dose may beformulated in animal models to achieve a circulating plasmaconcentration range that includes the IC₅₀ (i.e., the concentration ofthe test compound which achieves a half-maximal inhibition of symptoms)as determined in cell culture. Such information can be used to moreaccurately determine useful doses in humans. Levels in plasma may bemeasured, for example, by high performance liquid chromatography.

5.7.2. FORMULATIONS AND USE

Pharmaceutical compositions for use in accordance with the presentinvention may be formulated in conventional manner using one or morephysiologically acceptable carriers or excipients.

Thus, the compounds and their physiologically acceptable salts andsolvates may be formulated for administration by inhalation orinsufflation (either through the mouth or the nose) or oral, buccal,parenteral or rectal administration.

For oral administration, the pharmaceutical compositions may take theform of, for example, tablets or capsules prepared by conventional meanswith pharmaceutically acceptable excipients such as binding agents(e.g., pregelatinised maize starch, polyvinylpyrrolidone orhydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystallinecellulose or calcium hydrogen phosphate); lubricants (e.g., magnesiumstearate, talc or silica); disintegrants (e.g., potato starch or sodiumstarch glycolate); or wetting agents (e.g., sodium lauryl sulphate). Thetablets may be coated by methods well known in the art. Liquidpreparations for oral administration may take the form of, for example,solutions, syrups or suspensions, or they may be presented as a dryproduct for constitution with water or other suitable vehicle beforeuse. Such liquid preparations may be prepared by conventional means withpharmaceutically acceptable additives such as suspending agents (e.g.,sorbitol syrup, cellulose derivatives or hydrogenated edible fats);emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles(e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetableoils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates orsorbic acid). The preparations may also contain buffer salts, flavoring,coloring and sweetening agents as appropriate.

Preparations for oral administration may be suitably formulated to givecontrolled release of the active compound.

For buccal administration the compositions may take the form of tabletsor lozenges formulated in conventional manner.

For administration by inhalation, the compounds for use according to thepresent invention are conveniently delivered in the form of an aerosolspray presentation from pressurized packs or a nebuliser, with the useof a suitable propellant, e.g., dichlorodifluoromethane,trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide orother suitable gas. In the case of a pressurized aerosol the dosage unitmay be determined by providing a valve to deliver a metered amount.Capsules and cartridges of e.g. gelatin for use in an inhaler orinsufflator may be formulated containing a powder mix of the compoundand a suitable powder base such as lactose or starch.

The compounds may be formulated for parenteral administration byinjection, e.g., by bolus injection or continuous infusion. Formulationsfor injection may be presented in unit dosage form, e.g., in ampoules orin multi-dose containers, with an added preservative. The compositionsmay take such forms as suspensions, solutions or emulsions in oily oraqueous vehicles, and may contain formulatory agents such as suspending,stabilizing and/or dispersing agents. Alternatively, the activeingredient may be in powder form for constitution with a suitablevehicle, e.g., sterile pyrogen-free water, before use.

The compounds may also be formulated in rectal compositions such assuppositories or retention enemas, e.g., containing conventionalsuppository bases such as cocoa butter or other glycerides.

In addition to the formulations described previously, the compounds mayalso be formulated as a depot preparation. Such long acting formulationsmay be administered by implantation (for example subcutaneously orintramuscularly) or by intramuscular injection. Thus, for example, thecompounds may be formulated with suitable polymeric or hydrophobicmaterials (for example as an emulsion in an acceptable oil) or ionexchange resins, or as sparingly soluble derivatives, for example, as asparingly soluble salt.

The compositions may, if desired, be presented in a pack or dispenserdevice which may contain one or more unit dosage forms containing theactive ingredient. The pack may for example comprise metal or plasticfoil, such as a blister pack. The pack or dispenser device may beaccompanied by instructions for administration.

5.8. DIAGNOSIS OF CARDIOVASCULAR DISEASE ABNORMALITIES

A variety of methods may be employed, utilizing reagents such asfingerprint gene nucleotide sequences described in Section 5.4.1, andantibodies directed against differentially expressed and pathway genepeptides, as described, above, in Sections 5.4.2. (peptides) and 5.4.3.(antibodies). Specifically, such reagents may be used, for example, forthe detection of the presence of target gene mutations, or the detectionof either over or under expression of target gene mRNA.

The methods described herein may be performed, for example, by utilizingpre-packaged diagnostic kits comprising at least one specificfingerprint gene nucleic acid or anti-fingerprint gene antibody reagentdescribed herein, which may be conveniently used, e.g., in clinicalsettings, to diagnose patients exhibiting cardiovascular diseasesymptoms or at risk for developing cardiovascular disease.

Any cell type or tissue, preferably monocytes, endothelial cells, orsmooth muscle cells, in which the fingerprint gene is expressed may beutilized in the diagnostics described below.

5.8.1. DETECTION OF FINGERPRINT GENE NUCLEIC ACIDS

DNA or RNA from the cell type or tissue to be analyzed may easily beisolated using procedures which are well known to those in the art.Diagnostic procedures may also be performed “in situ” directly upontissue sections (fixed and/or frozen) of patient tissue obtained frombiopsies or resections, such that no nucleic acid purification isnecessary. Nucleic acid reagents such as those described in Section 5.1.may be used as probes and/or primers for such in situ procedures (see,for example, Nuovo, G. J., 1992, PCR in situ hybridization: protocolsand applications, Raven Press, NY).

Fingerprint gene nucleotide sequences, either RNA or DNA, may, forexample, be used in hybridization or amplification assays of biologicalsamples to detect cardiovascular disease-related gene structures andexpression. Such assays may include, but are not limited to, Southern orNorthern analyses, single stranded conformational polymorphism analyses,in situ hybridization assays, and polymerase chain reaction analyses.Such analyses may reveal both quantitative aspects of the expressionpattern of the fingerprint gene, and qualitative aspects of thefingerprint gene expression and/or gene composition. That is, suchaspects may include, for example, point mutations, insertions,deletions, chromosomal rearrangements, and/or activation or inactivationof gene expression.

Preferred diagnostic methods for the detection of fingerprintgene-specific nucleic acid molecules may involve for example, contactingand incubating nucleic acids, derived from the cell type or tissue beinganalyzed, with one or more labeled nucleic acid reagents as aredescribed in Section 5.1, under conditions favorable for the specificannealing of these reagents to their complementary sequences within thenucleic acid molecule of interest. Preferably, the lengths of thesenucleic acid reagents are at least 9 to 30 nucleotides. Afterincubation, all non-annealed nucleic acids are removed from the nucleicacid:fingerprint molecule hybrid. The presence of nucleic acids from thefingerprint tissue which have hybridized, if any such molecules exist,is then detected. Using such a detection scheme, the nucleic acid fromthe tissue or cell type of interest may be immobilized, for example, toa solid support such as a membrane, or a plastic surface such as that ona microtitre plate or polystyrene beads. In this case, after incubation,non-annealed, labeled fingerprint nucleic acid reagents of the typedescribed in Section 5.1. are easily removed. Detection of theremaining, annealed, labeled nucleic acid reagents is accomplished usingstandard techniques well-known to those in the art.

Alternative diagnostic methods for the detection of fingerprint genespecific nucleic acid molecules may involve their amplification, e.g.,by PCR (the experimental embodiment set forth in Mullis, K. B., 1987,U.S. Pat. No. 4,683,202), ligase chain reaction (Barany, F., 1991, Proc.Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication(Guatelli, J. C. et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878),transcriptional amplification system (Kwoh, D. Y et al., 1989, Proc.Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi, P. M. etal., 1988, Bio/Technology 6:1197), or any other nucleic acidamplification method, followed by the detection of the amplifiedmolecules using techniques well known to those of skill in the art.These detection schemes are especially useful for the detection ofnucleic acid molecules if such molecules are present in very lownumbers.

In one embodiment of such a detection scheme, a cDNA molecule isobtained from an RNA molecule of interest (e.g., by reversetranscription of the RNA molecule into cDNA). Cell types or tissues fromwhich such RNA may be isolated include any tissue in which wild typefingerprint gene is known to be expressed, including, but not limited,to monocytes, endothelium, and/or smooth muscle. A fingerprint sequencewithin the cDNA is then used as the template for a nucleic acidamplification reaction, such as a PCR amplification reaction, or thelike. The nucleic acid reagents used as synthesis initiation reagents(e.g., primers) in the reverse transcription and nucleic acidamplification steps of this method are chosen from among the fingerprintgene nucleic acid reagents described in Section 5.1. The preferredlengths of such nucleic acid reagents are at least 15-30 nucleotides.For detection of the amplified product, the nucleic acid amplificationmay be performed using radioactively or non-radioactively labelednucleotides. Alternatively, enough amplified product may be made suchthat the product may be visualized by standard ethidium bromide stainingor by utilizing any other suitable nucleic acid staining method.

In addition to methods which focus primarily on the detection of onenucleic acid sequence, fingerprint profiles, as discussed in Section5.5.4, may also be assessed in such detection schemes. Fingerprintprofiles may be generated, for example, by utilizing a differentialdisplay procedure, as discussed, above, in Section 5.1.2, Northernanalysis and/or RT-PCR. Any of the gene sequences described, above, inSection 5.4.1. may be used as probes and/or PCR primers for thegeneration and corroboration of such fingerprint profiles.

5.8.2. DETECTION OF FINGERPRINT GENE PEPTIDES

Antibodies directed against wild type or mutant fingerprint genepeptides, which are discussed, above, in Section 5.4.3, may also be usedas cardiovascular disease diagnostics and prognostics, as described, forexample, herein. Such diagnostic methods, may be used to detectabnormalities in the level of fingerprint gene protein expression, orabnormalities in the structure and/or tissue, cellular, or subcellularlocation of fingerprint gene protein. Structural differences mayinclude, for example, differences in the size, electronegativity, orantigenicity of the mutant fingerprint gene protein relative to thenormal fingerprint gene protein.

Protein from the tissue or cell type to be analyzed may easily beisolated using techniques which are well known to those of skill in theart. The protein isolation methods employed herein may, for example, besuch as those described in Harlow and Lane (Harlow, E. and Lane, D.,1988, “Antibodies: A Laboratory Manual”, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y.), which is incorporated herein byreference in its entirety.

Preferred diagnostic methods for the detection of wild type or mutantfingerprint gene peptide molecules may involve, for example,immunoassays wherein fingerprint gene peptides are detected by theirinteraction with an anti-fingerprint gene specific peptide antibody.

For example, antibodies, or fragments of antibodies, such as thosedescribed, above, in Section 5.4.3, useful in the present invention maybe used to quantitatively or qualitatively detect the presence of wildtype or mutant fingerprint gene peptides. This can be accomplished, forexample, by immunofluorescence techniques employing a fluorescentlylabeled antibody (see below) coupled with light microscopic, flowcytometric, or fluorimetric detection. Such techniques are especiallypreferred if the fingerprint gene peptides are expressed on the cellsurface.

The antibodies (or fragments thereof) useful in the present inventionmay, additionally, be employed histologically, as in immunofluorescenceor immunoelectron microscopy, for in situ detection of fingerprint genepeptides. In situ detection may be accomplished by removing ahistological specimen from a patient, and applying thereto a labeledantibody of the present invention. The antibody (or fragment) ispreferably applied by overlaying the labeled antibody (or fragment) ontoa biological sample. Through the use of such a procedure, it is possibleto determine not only the presence of the fingerprint gene peptides, butalso their distribution in the examined tissue. Using the presentinvention, those of ordinary skill will readily perceive that any of awide variety of histological methods (such as staining procedures) canbe modified in order to achieve such in situ detection.

Immunoassays for wild type or mutant fingerprint gene peptides typicallycomprise incubating a biological sample, such as a biological fluid, atissue extract, freshly harvested cells, or cells which have beenincubated in tissue culture, in the presence of a detectably labeledantibody capable of identifying fingerprint gene peptides, and detectingthe bound antibody by any of a number of techniques well known in theart.

The biological sample may be brought in contact with and immobilizedonto a solid phase support or carrier such as nitrocellulose, or othersolid support which is capable of immobilizing cells, cell particles orsoluble proteins. The support may then be washed with suitable buffersfollowed by treatment with the detectably labeled fingerprint genespecific antibody. The solid phase support may then be washed with thebuffer a second time to remove unbound antibody. The amount of boundlabel on solid support may then be detected by conventional means.

By “solid phase support or carrier” is intended any support capable ofbinding an antigen or an antibody. Well-known supports or carriersinclude glass, polystyrene, polypropylene, polyethylene, dextran, nylon,amylases, natural and modified celluloses, polyacrylamides, gabbros, andmagnetite. The nature of the carrier can be either soluble to someextent or insoluble for the purposes of the present invention. Thesupport material may have virtually any possible structuralconfiguration so long as the coupled molecule is capable of binding toan antigen or antibody. Thus, the support configuration may bespherical, as in a bead, or cylindrical, as in the inside surface of atest tube, or the external surface of a rod. Alternatively, the surfacemay be flat such as a sheet, test strip, etc. Preferred supports includepolystyrene beads. Those skilled in the art will know many othersuitable carriers for binding antibody or antigen, or will be able toascertain the same by use of routine experimentation.

The binding activity of a given lot of anti-wild type or mutantfingerprint gene peptide antibody may be determined according to wellknown methods. Those skilled in the art will be able to determineoperative and optimal assay conditions for each determination byemploying routine experimentation.

One of the ways in which the fingerprint gene peptide-specific antibodycan be detectably labeled is by linking the same to an enzyme and use inan enzyme immunoassay (EIA) (Voller, “The Enzyme Linked ImmunosorbentAssay (ELISA)”, Diagnostic Horizons 2:1-7, 1978, MicrobiologicalAssociates Quarterly Publication, Walkersville, Md.; Voller, et al., J.Clin. Pathol. 31:507-520 (1978); Butler, Meth. Enzymol. 73:482-523(1981); Maggio, (ed.) Enzyme Immunoassay, CRC Press, Boca Raton, Fla.,1980; Ishikawa, et al., (eds.) Enzyme Immunoassay, Kgaku Shoin, Tokyo,1981). The enzyme which is bound to the antibody will react with anappropriate substrate, preferably a chromogenic substrate, in such amanner as to produce a chemical moiety which can be detected, forexample, by spectrophotometric, fluorimetric or by visual means. Enzymeswhich can be used to detectably label the antibody include, but are notlimited to, malate dehydrogenase, staphylococcal nuclease,delta-5-steroid isomerase, yeast alcohol dehydrogenase,alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase,horseradish peroxidase, alkaline phosphatase, asparaginase, glucoseoxidase, beta-galactosidase, ribonuclease, urease, catalase,glucose-6-phosphate dehydrogenase, glucoamylase andacetylcholinesterase. The detection can be accomplished by colorimetricmethods which employ a chromogenic substrate for the enzyme. Detectionmay also be accomplished by visual comparison of the extent of enzymaticreaction of a substrate in comparison with similarly prepared standards.

Detection may also be accomplished using any of a variety of otherimmunoassays. For example, by radioactively labeling the antibodies orantibody fragments, it is possible to detect fingerprint gene wild typeor mutant peptides through the use of a radioimmunoassay (RIA) (see, forexample, Weintraub, B., Principles of Radioimmunoassays, SeventhTraining Course on Radioligand Assay Techniques, The Endocrine Society,March, 1986, which is incorporated by reference herein). The radioactiveisotope can be detected by such means as the use of a gamma counter or ascintillation counter or by autoradiography.

It is also possible to label the antibody with a fluorescent compound.When the fluorescently labeled antibody is exposed to light of theproper wave length, its presence can then be detected due tofluorescence. Among the most commonly used fluorescent labelingcompounds are fluorescein isothiocyanate, rhodamine, phycoerythrin,phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.

The antibody can also be detectably labeled using fluorescence emittingmetals such as ¹⁵²Eu, or others of the lanthanide series. These metalscan be attached to the antibody using such metal chelating groups asdiethylenetriaminepentacetic acid (DTPA) or ethylenediaminetetraaceticacid (EDTA).

The antibody also can be detectably labeled by coupling it to achemiluminescent compound. The presence of the chemiluminescent-taggedantibody is then determined by detecting the presence of luminescencethat arises during the course of a chemical reaction. Examples ofparticularly useful chemiluminescent labeling compounds are luminol,isoluminol, theromatic acridinium ester, imidazole, acridinium salt andoxalate ester.

Likewise, a bioluminescent compound may be used to label the antibody ofthe present invention. Bioluminescence is a type of chemiluminescencefound in biological systems in, which a catalytic protein increases theefficiency of the chemiluminescent reaction. The presence of abioluminescent protein is determined by detecting the presence ofluminescence. Important bioluminescent compounds for purposes oflabeling are luciferin, luciferase and aequorin.

5.8.3. IMAGING CARDIOVASCULAR DISEASE CONDITIONS

In some cases, differentially expressed gene products identified hereinmay be up-regulated under cardiovascular disease conditions andexpressed on the surface of the affected tissue. Such target geneproducts allow for the non-invasive imaging of damaged or diseasedcardiovascular tissue for the purposed of diagnosis and directing oftreatment of the disease. For example, such differentially expressedgene products may include but are not limited to atherosclerosisspecific adhesion molecules responsible for atherogenesis, or monocytescavenger receptors that are up-regulated in response to oxidized LDL,which are discussed in Section 2, above. Alternatively, other suchsurface proteins may be specifically up-regulated in tissues sufferingfrom ischemia/reperfusion or other tissues with atherosclerotic orrestenotic lesions.

As described in the example in Section 9, below, the rchd523 gene is agene that is up-regulated in endothelial cells under shear stress.Furthermore, the rchd523 gene encodes a novel G protein-coupledreceptor, containing an extracellular amino terminal domain, in additionto multiple transmembrane domains. The rchd523 gene product, therefore,provides an excellent tool for imaging cardiovascular diseaseconditions. An example illustrating the use of this method in accordancewith the invention is provided in Section 11, below.

Monoclonal antibodies, as described in Section 5.6.1.2, above, whichspecifically bind to such surface proteins, such as the rchd523 geneproduct, may be used for the diagnosis of cardiovascular disease by invivo tissue imaging techniques. An antibody specific for a target geneproduct, or preferably an antigen binding fragment thereof, isconjugated to a label (e.g., a gamma emitting radioisotope) whichgenerates a detectable signal and administered to a subject (human oranimal) suspected of having cardiovascular disease. After sufficienttime to allow the detectably-labeled antibody to localize at thediseased or damaged tissue site (or sites), the signal generated by thelabel is detected by a photoscanning device. The detected signal is thenconverted to an image of the tissue. This image makes it possible tolocalize the tissue in vivo. This data can then be used to develop anappropriate therapeutic strategy.

Antibody fragments, rather than whole antibody molecules, are generallypreferred for use in tissue imaging. Antibody fragments accumulate atthe tissue(s) more rapidly because they are distributed more readilythan are entire antibody molecules. Thus an image can be obtained inless time than is possible using whole antibody. These fragments arealso cleared more rapidly from tissues, resulting in a lower backgroundsignal. See, e.g., Haber et al., U.S. Pat. No. 4,036,945; Goldenberg etal., U.S. Pat. No. 4,331,647. The divalent antigen binding fragment(Fab′)₂ and the monovalent Fab are especially preferred. Such fragmentscan be prepared by digestion of the whole immunoglobulin molecule withthe enzymes pepsin or papain according to any of several well knownprotocols. The types of labels that are suitable for conjugation to amonoclonal antibody for diseased or damaged tissue localization include,but are not limited to radiolabels (i.e., radioisotopes), fluorescentlabels and biotin labels.

Among the radioisotopes that can be used to label antibodies or antibodyfragments, gamma-emitters, positron-emitters, X-ray-emitters andfluorescence-emitters are suitable for localization. Suitableradioisotopes for labeling antibodies include Iodine-131, Iodine-123,Iodine-125, Iodine-126, Iodine-133, Bromine-77, Indium-111, Indium-113m,Gallium-67, Gallium-68, Ruthenium-95, Ruthenium-97, Ruthenium-103,Ruthenium-105, Mercury-107, Mercury-203, Rhenium-99m, Rhenium-105,Rhenium-101, Tellurium-121m, Tellurium-122m, Tellurium-125m,Thulium-165, Thulium-167, Thulium-168, Technetium-99m and Fluorine-18.The halogens can be used more or less interchangeably as labels sincehalogen-labeled antibodies and/or normal immunoglobulins would havesubstantially the same kinetics and distribution and similar metabolism.

The gamma-emitters Indium-111 and Technetium-99m are preferred becausethese radiometals are detectable with a gamma camera and have favorablehalf lives for imaging in vivo. Antibody can be labelled with Indium-111or Technetium-99m via a conjugated metal chelator, such as DTPA(diethlenetriaminepentaacetic acid). See Krejcarek et al., 1977,Biochem. Biophys. Res. Comm. 77:581; Khaw et al., 1980, Science 209:295;Gansow et al., U.S. Pat. No. 4,472,509; Hnatowich, U.S. Pat. No.4,479,930, the teachings of which are incorporated herein by reference.

Fluorescent compounds that are suitable for conjugation to a monoclonalantibody include fluorescein sodium, fluorescein isothiocyanate, andTexas Red sulfonyl chloride. See, DeBelder & Wik, 1975, CarbohydrateResearch 44:254-257. Those skilled in the art will know, or will be ableto ascertain with no more than routine experimentation, otherfluorescent compounds that are suitable for labeling monoclonalantibodies.

6. EXAMPLE Identification of Genes Differently Expressed in Response toParadigm A: In Vitro Foam Cell Paradigm

According to the invention, differential display may be used to detectgenes that are differentially expressed in monocytes that were treatedso as to simulate the conditions under which foam cells develop duringatherogenesis.

6.1. MATERIALS AND METHODS

6.1.1. CELL ISOLATION AND CULTURING

Blood (˜200 ml) was drawn into chilled 20 ml vacutainer tubes to which 3ml of citrate phosphate dextrose (Sigma) was added. Blood was thenpooled into 50 ml tubes and spun in the Beckman GS-6R at 1250 RPM for 15minutes at 4° C. The upper clear layer (˜25 ml) was then removed with apipette and discarded and replaced with the same volume of 4° C. PBS.The blood was then mixed, and spun again at 2680 RPM for 15 minutes at4° C. The upper layer was then removed and discarded, and the buffy coatat the interface was removed in ˜5 ml and placed in a separate 50 mltube, and the pipette was washed with 20 ml PBS. Cells were added to a Tflask and stored at 4° C. for 16 hours. A small aliquot of the cellswere then removed and counted using a hemacytometer. The final red bloodcell concentration in the buffy coat population was then adjusted to1.5×10⁹/ml with PBS, the cells were added to Leucoprep tubes (BectonDickinson) after being allowed to come to room temperature, and spun at2300 RPM for 25 minutes at 25° C. The upper clear layer was removed anddiscarded and the turbid layer over the gel was removed and pooled in 50ml tubes. Samples were then diluted to 50 ml with PBS (25° C.) and spunat 1000 RPM for 10 minutes. The supernatant was then removed, and thepellet was resuspended in 50 ml PBS. This procedure was repeated 3 moretimes. After the last spin, the cells were resuspended in a small volumeof PBS and counted.

Tissue culture dishes were coated with bovine collagen before monocyteswere plated out. 1/6 volume of 7X RPMI (JRH Biosciences) was added toVitrogen 100 collagen (Celtrix) which was then diluted 1:10 with RPMI toa final concentration of 0.35 mg/ml. Collagen mixture was then added toplates (2.5 ml/100 mm dish) and placed at 37° C. for at least one hourto allow for gel formation. After gel formation has taken place, theRPMI was removed and cells were added in RPMI/10% plasma derived serum(PDS). PDS was prepared by drawing blood into chilled evacuated tubescontaining 1/10th volume 3.8% sodium citrate. Blood was then transferredinto new Sorvall tubes and spun at 14,000-16,000 RPM for 20 minutes at4° C. Plasma layer was removed and pooled in new tubes to which 1/50thvolume 1M CaCl₂ was added. Plasma was mixed and aliquoted into newSorvall tubes and incubated at 37° for 2 hours to allow for fibrin clotformation. The clot was then disturbed with a pipette to allow it tocontract and tubes were spun at 14,500 RPM for 20 minutes at 25° C.Supernatant was collected, pooled, and heat inactivated at 56° C. priorto sterile filtration and freezing.

Purified human monocytes were cultured in 10% PDS/RPMI containing 5units/ml of Genzyme recombinant human MCSF for 5 days before beingtreated with LDL, oxidized LDL, acetylated LDL (all LDL at 50 μg/ml),lysophosphatidylcholine (Sigma, 37.5 μM), or homocysteine (Sigma, 1 mM).After incubation with these reagents for periods ranging from 2 hours upto 3 days, the media was withdrawn and the cells were dissolved in RNAlysis buffer and RNA was prepared as described, above, in Section 6.1.

Lipoproteins

For oxidation, human LDL (Sigma) was first diluted to 1 mg/ml with PBSand then dialyzed against PBS at 4° C. overnight. LDL was then dilutedto 0.3 mg/ml with PBS. CuSO₄·5H₂O was then added to 5 uM finalconcentration, and the solution was incubated in a T flask in a 37° C.incubator for 24 hr. LDL solution was then dialyzed at 4° C. against0.15M NaCl/0.3 mM EDTA for 2 days with several changes, before beingremoved and concentrated using an Amicon spin column by spinning for 1hr. 4000 RPM at 4° C.

For acetylation, 1 ml of 5 mg/ml LDL was added to 1 ml of a saturatedsolution of NaOAc in a 15 ml tube on ice on a shaker at 4° C. 8 μl ofacetic anhydride was added 2 μl at a time over 1 hr. LDL was thendialyzed for 48 hr. against 0.15M NaCl/0.3 mM EDTA at 4° C. for 48 hr.with several changes. Final concentrations of derivatized LDL's weredetermined by comparing to a dilution curve of native LDL analyzed atOD₂₈₀, with 0.15M NaCl/0.3 mM EDTA used as diluent in all cases.

6.1.2. ANALYSIS OF PARADIGM MATERIAL Differential Display

Removal of DNA:

The RNA pellet was resuspended in H₂O and quantified byspectrophotometry at OD₂₆₀. Approximately half of the sample was thentreated with DNAse I to remove contaminating chromosomal DNA. RNA wasamplified by PCR using the following procedure. 50 ul RNA sample (10-20μg), 5.7 μl 10x PCR buffer (Perkin-Elmer/Cetus), 1 μl RNAse inhibitor(40 units/μl) (Boehringer Mannheim, Germany) were mixed together,vortexed, and briefly spun. 2 μl DNAse I (10 units/μl) (BoehringerMannheim) was added to the reaction which was incubated for 30 min. at37° C. The total volume was brought to 200 μl with DEPC H₂O, extractedonce with phenol/chloroform, once with chloroform, and precipitated byadding 20 μl 3M NaOAc, pH 4.8, (DEPC-treated), 500 μl absolute ETOH andincubating for 1 hour on dry ice or −20° C. overnight. The precipitatedsample was centrifuged for 15 min., and the pellet was washed with 70%ETOH. The sample was re-centrifuged, the remaining liquid was aspirated,and the pellet was resuspended in 100 μl H₂O. The concentration of RNAwas measured by reading the OD₂₆₀.

First strand cDNA synthesis:

For each RNA sample duplicate reactions were carried out in parallel.400 ng RNA plus DEPC H₂O in a total volume of 10 μl were added to 4 μlT₁₁XX (SEQ ID NO:31) reverse primer (10 μM) (Operon). The specificprimers used in each experiment are provided in the Description of theFigures in Section 4, above. The mixture was incubated at 70° C. for 5min. to denature the RNA and then placed at r.t. 26 μl of reaction mixcontaining the following components was added to each denaturedRNA/primer sample: 8 μl 5x First Strand Buffer (Gibco/BRL, Gaithersburg,Md.), 4 μl 0.1M DTT (Gibco/BRL), 2 μl RNAse inhibitor (40 units/μl)(Boehringer Mannheim), 4 μl 200 μM dNTP mix, 6 μl H₂O, 2 μl Superscriptreverse transcriptase (200 units/μl) (Gibco/BRL). The reactions weremixed gently and incubated for 30 min. at 42° C. 60 μl of H₂O (finalvolume=100 μl) were then added and the samples were denatured for 5 min.at 85° C. and stored at −20° C.

PCR reactions:

13 μl of reaction mix was added to each tube of a 96 well plate on ice.The reaction mix contained 6.4 μl H₂O, 2 μl 10x PCR Buffer(Perkin-Elmer), 2 μl 20 μM dNTP's, 0.4 μl ³⁵S dATP (12.5 μCi/μl; 50 μCitotal) (Dupont/NEN), 2 μl forward primer (10 μM) (Operon), and 0.2 μlAmpliTaq Polymerase (5 units/μl) (Perkin-Elmer). Next, 2 μl of reverseprimer (T₁₁XX, 10 μM) were added to the side of each tube followed by 5μl of cDNA also to the sides of the tubes, which were still on ice. Thespecific primers used in each experiment are provided in the Descriptionof the Figures in Section 4, above. Tubes were capped and mixed, andbrought up to 1000 RPM in a centrifuge then returned immediately to ice.The PCR machine (Perkin-Elmer 9600) was programmed for differentialdisplay as follows:

94° C.  2 min. *94° C. 15 sec. *40° C.  2 min. *ramp 72° C.  1 min. *72°C. 30 sec. 72° C.  5 min. 4° C. hold *X40

When the PCR machine reached 94° C., the plate was removed from ice andplaced directly into the Perkin-Elmer 9600 PCR machine . Following PCR,15 μl of loading dye, containing 80% formamide, 10 mM EDTA, 1 mg/mlxylene cyanol, 1 mg/ml bromphenol blue were added. The loading dye andreaction were mixed, incubated at 85° C. for 5 min., cooled on ice,centrifuged, and placed on ice. Approximately 4 μl from each tube wereloaded onto a prerun (60 V) 6% acrylamide gel. The gel was run atapproximately 80 V until top dye front was about 1 inch from bottom. Thegel was transferred to 3 MM paper (Whatman Paper, England) and driedunder vacuum. Bands were visualized by autoradiography.

Band isolation and amplification:

Differentially expressed bands were excised from the dried gel with arazor blade and placed into a microfuge tube with 100 μl H₂O and heatedat 100° C. for 5 min., vortexed, heated again to 100° C. for 5 min., andvortex again. After cooling, 100 μl H₂O, 20 μl 3M NaOAc, 1 μl glycogen(20 mg/ml), and 500 μl ethanol were added and chilled. Aftercentrifugation, the pellet was washed and resuspended in 10 μl H₂O.

The isolated differentially expressed bands were then amplified by PCRusing the following reaction conditions:

58 μl H₂O 10 μl 10x PCR Buffer 10 μl 200 μm dNTP's 10 μl 10 μM reverseprimer 10 μl 10 μM forward primer 1.5 μl amplified band 0.5 μl AmpliTaqpolymerase (5 units/μl) (Perkin Elmer)

PCR was performed using the program described in this Section, above,for differential display. After PCR, glycerol loading dyes were addedand samples were loaded onto a 2% preparative TAE/Biogel (Bio101, LaJolla, Calif.) agarose gel and eluted. Bands were then excised from thegel with a razor blade and vortexed for 15 min. at r.t., and purifiedusing the Mermaid kit from Bio101 by adding 3 volumes of Mermaid highsalt binding solution and 8 μl of resuspended glassfog in a microfugetube. Glassfog was then pelleted, washed 3 times with ethanol washsolution, and then DNA was eluted twice in 10 μl at 50° C.

Subcloning:

The TA cloning kit (Invitrogen, San Diego, Calif.) was used to subclonethe amplified bands. The ligation reaction typically consisted of 4 μlsterile H₂O, 1 μl ligation buffer, 2 μl TA cloning vector, 2 μl PCRproduct, and 1 μl T4 DNA ligase. The volume of PCR product can vary, butthe total volume of PCR product plus H₂O was always 6 μl. Ligations(including vector alone) were incubated overnight at 12° C. beforebacterial transformation. TA cloning kit competent bacteria (INVαF′:enda1, recAl, hsdRl7 (r−k, m+k), supE44, λ−, thi−1, gyrA, relA1,φ80lacZαΔM15Δ (lacZYA-argF), deoR+, F′) were thawed on ice and 2 μl of0.5 M β-mercaptoethanol were added to each tube. 2 μl from each ligationwere added to each tube of competent cells (50 μl), mixed withoutvortexing, and incubated on ice for 30 min. Tubes were then placed in42° C. bath for exactly 30 sec., before being returned to ice for 2 min.450 μl of SOC media (Sambrook et al., 1989, supra) were then added toeach tube which were then shaken at 37° C. for 1 hr. Bacteria were thenpelleted, resuspended in ˜200 μl SOC and plated on Luria broth agarplates containing X-gal and 60 μg/ml ampicillin and incubated overnightat 37° C. White colonies were then picked and screened for inserts usingPCR.

A master mix containing 2 μl 10x PCR buffer, 1.6 μl 2.5 mM dNTP's, 0.1μl 25 mM MgCl₂, 0.2 μl M13 reverse primer (100 ng/μl), 0.2 μl M13forward primer (100 ng/μl), 0.1 μl AmpliTaq (Perkin-Elmer), and 15.8 μlH₂O was made. 40 μl of the master mix were aliquoted into tubes of a 96well plate, and whole bacteria were added with a pipette tip prior toPCR. The PCR machine (Perkin-Elmer 9600) was programmed for insertscreening as follows:

94° C.  2 min. *94° C. 15 sec. *47° C.  2 min. *ramp 72° C. 30 sec. *72°C. 30 sec. 72° C. 10 min. 4° C. hold * = X35

Reaction products were eluted on a 2% agarose gel and compared to vectorcontrol. Colonies with vectors containing inserts were purified bystreaking onto LB/Amp plates. Vectors were isolated from such strainsand subjected to sequence analysis, using an Applied BiosystemsAutomated Sequencer (Applied Biosystems, Inc. Seattle, Wash.).

Northern analysis:

Northern analysis was performed to confirm the differential expressionof the genes corresponding to the amplified bands. The probes used todetect mRNA were synthesized as follows: typically 2 μl amplified band(˜30 ng), 7 μl H₂O, and 2 μl 10x Hexanucleotide mix(Boehringer-Mannheim) were mixed and heated to 95° C. for 5 min., andthen allowed to cool on ice. The volume of the amplified band can vary,but the total volume of the band plus H₂O was always 9 μl. 3 μldATP/dGTP/dTTP mix (1:1:1 of 0.5 mM each), 5 μl α³²P dCTP 3000 Ci/mM (50μCi total) (Amersham, Arlington Heights, Ill.), and 1 μl Klenow (2units) (Boehringer-Mannheim) were mixed and incubated at 37° C. After 1hr., 30 μl TE were added and the reaction was loaded onto a Biospin-6™column (Biorad, Hercules, Calif.), and centrifuged. A 1 μl aliquot ofeluate was used to measure incorporation in a scintillation counter withscintillant to ensure that 10⁶ cpm/μl of incorporation was achieved.

The samples were loaded onto a denaturing agarose gel. A 300 ml 1% gelwas made by adding 3 g of agarose (SeaKem™ LE, FMC BioProducts,Rockland, Me.) and 60 ml of 5x MOPS buffer to 210 ml sterile H2O. 5xMOPS buffer (0.1M MOPS (pH 7.0), 40 mM NaOAc, 5 mM EDTA (pH 8.0)) wasmade by adding 20.6 g of MOPS to 800 ml of 50 mM NaOAc (13.3 ml of 3MNaOAc pH 4.8 in 800 ml sterile H₂O); then adjusting the pH to 7.0 with10M NaOH; adding 10 ml of 0.5M EDTA (pH8.0); and adding H₂O to a finalvolume of 1 L. The mixture was heated until melted, then cooled to 50°C., at which time 5 μl ethidium bromide (5 mg/ml) and 30 ml of 37%formaldehyde of gel were added. The gel was swirled quickly to mix, andthen poured immediately.

2 μg RNA sample, 1x final 1.5x RNA loading dyes (60% formamide, 9%formaldehyde, 1.5X MOPS, 0.075% XC/BPB dyes) and H₂O were mixed to afinal volume of 40 μl. The tubes were heated at 65° C. for 5 min. andthen cooled on ice. 10 μg of RNA MW standards (New England Biolabs,Beverly, Mass.) were also denatured with dye and loaded onto the gel.The gel was run overnight at 32 V in MOPS running buffer.

The gel was then soaked in 0.5 μg/ml Ethidium Bromide for 45 min., 50 mMNaOH/0.1 M NaCl for 30 min., 0.1 M Tris pH 8.0 for 30 min., and 20x SSCfor 20 min. Each soaking step was done at r.t. with shaking. The gel wasthen photographed along with a fluorescent ruler before blotting withHybond-N membrane (Amersham), according to the methods of Sambrook etal., 1989, supra, in 20x SSC overnight.

For hybridization, the blot was placed into a roller bottle containing10 ml of prehybridization solution consisting of 50% formamide and 1xDenhardt's solution, and placed into 65° C. incubator for 30 min. Theprobe was then heated to 95° C., chilled on ice, and added to 10 ml ofhybridization solution, consisting of 50% formamide, 1x Denhardt'ssolution, 10% dextransulfate, to a final concentration of 10⁶ cpm/ml.The prehybridization solution was then replaced with the probe solutionand incubated overnight at 42° C. The following day, the blot was washedthree times for 30 min. in 2x SSC/0.1% SDS at room temperature beforebeing covered in plastic wrap and put down for exposure.

RT-PCR Analysis:

RT-PCR was performed to detect differentially expressed levels of mRNAfrom the genes corresponding to amplified bands. First strand synthesiswas conducted by mixing 20 μl DNased RNA (˜2 μg), 1 μl oligo dT (Operon)(1 μg), and 9.75 μl H₂O. The samples were heated at 70° C. for 10 min.,and then allowed to cool on ice. 10 μl first strand buffer (Gibco/BRL),5 μl 0.1M DTT, 1.25 μl 20 mM dNTP's (500 μM final), 1 μl RNAsin (40units/μl) (Boehringer Mannheim), and 2 μl Superscript ReverseTranscriptase (200 units/μl) (Gibco/BRL) were added to the reaction,incubated at 42° C. for 1 hr., and then placed at 85° C. for 5 min., andstored at −20° C.

PCR was performed on the reverse transcribed samples. Each reactioncontained 2 μl 10x PCR buffer, 14.5 μl H₂O, 0.2 μl 20 mM dNTP's (200 μMfinal), 0.5 μl 20 μM forward primer (0.4 μM final), 0.5 μl 20 μM reverseprimer (0.4 μM final), 0.3 μl AmpliTaq polymerase (Perkin-Elmer/Cetus),2 μl cDNA dilution or positive control (˜40 pg). The specific primersused in each experiment are provided in the Description of the Figuresin Section 4, above. Samples were placed in the PCR 9600 machine at 94°C. (hot start), which was programmed as follows:

94° C. 2 min. (samples loaded) *94° C. 45 sec. *55° C. 45 sec. *72° C. 2min. 72° C. 5 min. 4° C. hold *35x

Reactions were carried out on cDNA dilution series and tubes wereremoved at various cycles from the machine during 72° C. step. Reactionproducts were eluted on a 1.8% agarose gel and visualized with ethidiumbromide.

6.1.3. CHROMOSOMAL LOCALIZATION OF TARGET GENES

Once the nucleotide sequence has been determined, the presence of thegene on a particular chromosome is detected. Oligonucleotide primersbased on the nucleotide sequence of the target gene are used in PCRreactions using individual human chromosomes as templates. Individualsamples of each the twenty-three human chromosomes are commerciallyavailable (Coriel Institute for Medical Research, Camden, N.J.). Thechromosomal DNA is amplified according to the following conditions: 10ng chromosomal DNA, 2 μl 10x PCR buffer, 1.6 μl 2.5 mM dNTP's, 0.1 μl 25mM MgCl₂, 0.2 μl reverse primer (100 ng/μl), 0.2 μl forward primer (100ng/μl), 0.1 μl Taq polymerase, and 15.8 μl H₂O. Samples are placed inthe PCR 9600 machine at 94° C. (hot start), which is programmed asfollows:

94° C.  2 min. (samples loaded) *94° C. 20 sec. *55° C. 30 sec. *72° C.30 sec. 72° C.  5 min. 4° C. hold *35x

7. EXAMPLE Identification of Genes Differentially Expressed in Responseto Paradigm B: In Vivo Monocytes

In an alternative embodiment of the invention, genes differentiallyexpressed in monocytes were detected under highly physiologicallyrelevant, in vivo conditions. According to Paradigm B, human subjectswere held in a clinical setting and the fat/cholesterol content of theirdiets was controlled. Monocytes were isolated at different stages oftreatment, and their gene expression pattern was compared to that ofcontrol groups.

By use of Paradigm B, the human bcl-2 gene was identified. Itsexpression decreases in response to the atherogenic conditions of highfat/high cholesterol (FIG. 1). The Apo E-/- mouse is the first mousemodel of atherosclerosis with pathology similar to that of human plaquedevelopment (Plump et al., 1992, Cell 71: 343-353). Serum cholesterollevels in these mice on a chow diet is five times higher than those ofcontrol littermates. To address whether the regulation of the mousebcl-2 gene is also affected by serum cholesterol levels, monocytes fromapoE-deficient mice and littermate wild-type controls were purified andmouse bcl-2 mRNA levels were compared using quantitative RT-PCR. By thismethod, mouse bcl-2 mRNA levels were significantly lower in theapoE-deficient mice relative to the wild-type controls (FIG. 3).

The differential expression pattern of the human glutathione peroxidasegene (HUMGPXP1) was also discovered. The differential expression ofHUMGPXP1 was initially detected in a preliminary detection system,described, below, in Section 7.1.2. Once HUMGPXP1 sequences wereobtained, the gene's differential expression pattern was verified andcharacterized under the physiologically relevant conditions of ParadigmB. Glutathione peroxidase is known to be involved in the removal oftoxic peroxides that form in the course of growth and metabolism undernormal aerobic conditions and under oxidative stress. Human plasmaglutathione peroxidase gene was originally isolated from a humanplacenta cDNA library (Takahashi et al., 1990, J. Biochem. 108:145-148). It has been shown to be expressed in two human cell lines ofthe myeloid lineage (Porter et al., 1992, Clinical Science 83: 343-345).Other studies have also linked reduced levels of this enzyme with heartattack risk (Guidi, et al., 1986, J. Clin. Lab Invest. 46: 549-551; Wanget al., 1981, Klin. Wochenschr. 59: 817-818; Kok et al., 1989, J. Am.Med. Assoc. 261: 1161-1164; and Gromadzinska & Sklodowska, 1990, J. Am.Med. Assoc. 263: 949-950). Glutathione peroxidase has not beenpreviously known to be down-regulated in human monocytes undercardiovascular disease conditions, as described herein.

Interestingly, bcl-2 has been recognized as playing a key role inpreventing apoptosis, and expression of glutathione peroxidase in theabsence of bcl-2 is able to compensate for this loss by preventingapoptosis (Hockenbery et al., 1993, Cell 75: 241-251). These findingsregarding bcl-2 and HUMGPXP1, described herein in this section,suggested a novel role for the monocyte in plaque formation whichinvolves apoptosis induction caused by high LDL concentrations insidethe cell, or perhaps by oxidative stress in the cell mediated byoxidized LDL.

To confirm this relationship between apoptosis and atherosclerosis, theability of bcl-2 expression to ameliorate atherosclerosis is tested.Because bcl-2 is normally down-regulated under atherogenic conditions, atransgenic mouse strain is engineered in which the human bcl-2 gene isexpressed under the control of the scavenger receptor promoter, which isinduced in monocyte foam cells under atherogenic conditions. Thistransgenic mouse is then crossed with an apoE-deficient atheroscleroticmouse model. The ability of the increased expression of the bcl-2 targetgene to ameliorate atherosclerosis is demonstrated by a decrease ininitiation and progression of plaque formation observed in thetransgenic apoE-deficient mouse.

The identification of the differential expression of these genes,therefore, provides targets for the treatment and diagnosis ofcardiovascular disease. Intervening in the apoptotic pathway throughBcl-2 and glutathione peroxidase, may lead to lesion regression orprevention of plaque formation, or both. Furthermore, the discovery of aconnection between the apoptotic pathway and atherosclerosisdemonstrates the effectiveness of the methods described herein inidentifying the full panoply of gene products that are involved in theatherosclerotic disease process. Furthermore, the down-regulation ofbcl-2 and HUMGPXP1 under Paradigm B provides a fingerprint for the studyof the effect of excess LDL on monocytes.

7.1. MATERIALS AND METHODS

7.1.1. IN VIVO CHOLESTEROL STUDIES

Patients were held in a clinical setting for a total of 9 weeks duringwhich time their lipid intake was very tightly controlled. There were atotal of 3 diets, and each patient was held on each diet for 3 weeks.Patients were healthy young (third decade of life) individuals with nohistory or symptoms of heart disease or dislipidemias. The 3 diets aredescribed below:

American Heart Association Diet II fat 25% cholesterol 80 mg/1000 kCalpolyunsaturated/saturated fat 1.5 Average American Diet fat 43%cholesterol 200 mg/1000 kCal polyunsaturated/saturated fat 0.34Combination Diet fat 43% cholesterol 80 mg/1000 kCalpolyunsaturated/saturated fat 0.34

The 3 diets were isocaloric, and the individual components of each dietmay vary with the participant's preference as long as the lipid levelsin the diet were a maintained.

Cell Isolation

At the end of each 3 week diet period, blood was drawn from each patientafter a 12 hour period of fasting and monocytes were purified. 50 ml ofblood was drawn into 5 evacuated tubes containing 1.4 ml each of citratephosphate dextrose to prevent coagulation. Blood was pooled into 50 mltubes and spun at 400 g (1250 RPM/Sorvall RC3B) for 15 minutes at 4° C.The upper serum layer (˜25 ml) was then removed with a pipette andreplaced with phosphate buffered saline (PBS) at 4° C. The blood wasmixed and then spun at 1850 x g (2680 RPM) for 15 minutes at 4° C. Mostof the clear upper layer was removed with a pipette, before the buffycoat at the interface was taken in ˜5 ml. The buffy coat was placed intoa separate 50 ml tube, and the pipette used to remove it was washed with20 ml PBS. A small aliquot of these cells was then diluted 1:1000 in PBSand counted under a microscope using a hemacytometer. Red blood cellconcentration was then adjusted with PBS to a final concentration of1.5×10⁹/ml, and 10 ml aliquots were added to Leucoprep Becton Dickinson)tubes for monocyte isolation. Tubes were spun for 25 minutes at 25° C.in a Sorvall RT6000 with the brake off. Most of the clear upper layerwas discarded, and the turbid layer above the gel was saved and pooledin 50 ml tubes. The volume of each tube was then increased to 50 ml with25° C. PBS, and spun at 1000 RPM (Sorvall RC3B) for 10 minutes at 4° C.The liquid was then discarded, the pellet was resuspended in 50 ml PBS,and spun again. This process was repeated 3 more times. The final cellpellet was then resuspended in 2 ml RNA lysis buffer (Sambrook et al.,1989, supra) and frozen for subsequent RNA isolation as described abovein Section 6.1.1.

Differential display, Northern analysis, RT-PCR, subcloning, and DNAsequencing were carried out as described, above, in Section 6.1.2.

7.1.2. PRELIMINARY DETECTION SYSTEM

The preliminary detection system described in this section was used toidentify sequences that are differentially expressed in a readilyassayed, in vitro system. Sequences that showed some homology to thosethought to be involved in cardiovascular disease were then used asspecific primers or probes, or both, in Paradigm B, wherein thedifferential expression was ascertained under physiologically relevantconditions, as described in section 7.1.1, above.

Cell culture

Blood (˜100 ml) was drawn from healthy human donors into vacutainertubes containing heparin (Becton Dickinson). Blood was diluted 1:1 withPD (Phosphate buffered saline (PBS) without Ca or Mg, plus 0.3 mM EDTA),and layered onto Ficoll (Lymphocyte Separation Media-Organon Teknikon)as 30 ml of blood/7 ml ficoll in a 50 ml blue-capped Falcon tube, andcentrifuged at 2000 RPM for 25 min. at room temperature (r.t.). Thebuffy coat was removed with a pipette, transferred to another 50 mltube, diluted to 30 ml with PD, and centrifuged at 1200 RPM for 10 min.at r.t. The pellet was resuspended in 30 ml PD and the previouscentrifugation step was repeated. The pellet was resuspended in 40 mlRPMI (2 mM 1-Glutamine+penicillin/streptomycin), plated onto 4 plates,and incubated at 37° C. for 2 hours. Supernatant was removed, and theplates were washed 3x with PBS at 37° C. Plates were finally resuspendedin 10 ml each with RPMI/20% human AB serum (Sigma, St. Louis, Mo.). Onday 5, the media was changed and 100 units/ml of human γ-IFN (Genzyme)were added. On day 7, the media was removed and replaced with RPMI/20%human LDL-deficient serum+100 units/ml of human γ-IFN. Native, oxidized,and acetylated LDL were each added to one plate with the fourth plateserving as control. After the specified incubation time (5 hr. or 24hr.) the media was removed and the cells were resuspended in 2 mlguanidine isothiocyanate RNA lysis buffer (Sambrook et al., 1989,supra). Lysed cells were then syringed with 23 G. needle, layered over5.7M CsCl, and centrifuged for 20 hr. at 35K RPM. RNA was isolatedaccording to the method of Sambrook et al., 1989, supra.

Lipoproteins were prepared as described, above, in section 6.1.1.Differential display, Northern analysis, RT-PCR, subcloning, and DNAsequencing were carried out as described, above, in Section 6.1.2. Fordifferential display, the primers used were T₁₁CC (reverse) and OPE4(forward), consisting of 5′GTGACATGCC3′ (SEQ ID NO:33). For RT-PCR, thefirst strand cDNA was primed with T₁₁CC (SEQ ID NO:32), and PCRreactions were carried out with rfhma15 primers(for-catgcctgtagaaaaaggtt; SEQ ID NO:34/rev-cttcatagaatctaagccta SEQ IDNO:35), and mouse γactin primers(for-cctgatagatgggcactgtgt/rev-gaacacggcattgtcactaact).

7.1.3. TRANSGENIC ApoE-DEFICIENT MOUSE EXPRESSING HUMAN bcl-2

Transgenic mice bearing a construct (FIG. 31) with the mouse scavengerreceptor regulatory element (5 kb) (M. Freeman, et al., 1995,unpublished results) driving expression of the human bcl-2 gene (hbcl-2)were produced. The scavenger receptor regulatory element (ScR) is knownto activate reporter gene expression in peritoneal macrophages intransgenic mice (M. Freeman, 1995, unpublished results). This 5 kbfragment is linked to the human bcl-2 cDNA (Cleary, et al., 1986, supra)via a NotI restriction site. Human growth hormone (hGH) sequences (Mayo,et al., 1983, Nature 306: 86-88) are then ligated onto the 3′ end ofthis construct through filled-in BamHI and EcoRV sites to providemessage stability. This construct is then digested with XhoI and the 9kb ScR-hbcl2-hGH sequences are purified away from vector sequences.Another plasmid sample is digested with KpnI to yield a fragment withonly 1.5 kb of scavenger receptor regulatory sequences which provide alower level of expression. These fragments are then injectedindependently into mouse embryos derived from the FVB and C57BL/6 mousestrains according to standard protocols (Hogan, et al., Manipulating theMouse Embryo, 1994, Cold Spring Harbor Laboratory Press). Followingbirth, tail sections are cut from mice derived from injected embryos andanalyzed for the presence of transgene sequences using hbcl-2 sequencesas probes on Southern blots.

Transgenic mice bearing the ScR-hbcl2-hGH construct are then bred towild-type mice of the same respective strain, and then the offspring arebackcrossed to produce homozygous lines of mice. These mice are thenbred to apoE-deficient mice. Offspring are analyzed for presence of theScR-hbcl2-hGH by preparing tail sections and probing with hbcl-2sequences on Southern blots. Offspring are then analyzed for lesionformation and progression according to the methods of Plump, et al.,1992, supra.

7.2. RESULTS

Differential display analysis was carried out on monocyte RNA derivedfrom the blood of patients whose serum cholesterol levels weremanipulated through fat/cholesterol intake in their diets. FIG. 1 showsband #14 which was present in the low dietary fat/low serum cholesterolconditions and goes away in the high dietary fat/high serum cholesterolconditions. When a radioactively labeled probe was prepared from band#14 and hybridized with a Northern blot prepared from RNA from the samepatient (FIG. 2), an 8 kb band was seen which was present in low serumcholesterol and disappeared in high serum cholesterol conditions. Whenband #14 sequences were subcloned, sequenced, and compared with thesequence database a 98% (203/207 bp) sequence similarity with the humanbcl-2 gene (Cleary et al., 1986, Cell 47, 19-28) was obtained,indicating that band #14 is bcl-2.

Glutathione peroxidase (HUMGPXP1) in expression in monocytes wasexamined to determine its physiological relationship to bcl-2.Differential expression of HUMGPXP1 was first detected in a preliminarydetection system using monocytes cultured in vitro. Human monocytes wereprepared as described above in subsection 7.1.2. Cells were lysed after5 hours and RNA was prepared. Differential display analysis was carriedout, and regulated bands were isolated and characterized. The DNAsequence was determined from a number of independent subclones ofamplified sequences of one such regulated band designated band 15. Usingthe BLAST program (Altschul, et al., 1990, J. Mol. Biol. 215: 403-410),a 176/177 (99%) sequence similarity was found between band 15 a sequencefor human plasma glutathione peroxidase exon 1 (HUMGPXP1). This sequenceoccurs upstream of the reported transcription start site. Nonetheless,RT-PCR analysis confirmed that the band 15 sequences are in fact withinthe same transcription unit as sequences downstream of the reportedtranscription start site.

Based on this preliminary result, the gene expression pattern ofglutathione peroxidase (HUMGPXP1) was further analyzed for verificationand characterization in physiologically relevant samples according toParadigm B. Monocytes derived from human blood under atherogenicconditions (high serum cholesterol) and healthy conditions (low serumcholesterol) were examined with RT-PCR. As shown in FIG. 4, thereappears to be 2-3 fold less cDNA amplified by the HUMGPXP1 primers fromthe high fat/cholesterol monocytes than in the low fat/cholesterolmonocytes, while the actin control bands are the same.

Monocytes from apoE-deficient mice and littermate wild-type controlswere purified and mouse bcl-2 mRNA levels were compared usingquantitative RT-PCR. By this method, mouse bcl-2 mRNA levels weresignificantly lower in the apoE-deficient mice relative to the wild-typecontrols (FIG. 3).

These results demonstrate that bcl-2 is an excellent target gene forintervening in lesion formation and development. It was previously knownthat, under normal conditions, bcl-2 expression prevents apoptosis. Theobserved down-regulation of bcl-2 caused by atherogenic conditions,therefore, provides an explanation of how such atherogenic conditionsmay lead to plaque formation. By down-regulating the normally protectivebcl-2 gene, high serum cholesterol triggers a series of events,entailing the induction of the apoptotic pathway, which results inprogrammed cell death, which in turn causes an inflammatory response andsubsequent plaque formation.

This model may be tested by counteracting the observed down-regulationof bcl-2. The human bcl-2 gene is placed in the ScR-hbcl2-hGH constructin which it is transcribed by a promoter that is activated in monocytefoam cells under atherogenic conditions. This construct is thenintroduced into an apoE-deficient mouse that otherwise serves as a modelfor atherosclerosis. The effect of bcl-2 expression on atherosclerosisis evidenced by the reduction in plaque initiation and development inthe apoE-deficient mice bearing the construct. Amelioration ofatherosclerosis may, therefore, be accomplished by such intervention inthe down-regulation of the bcl-2 target gene.

8. EXAMPLE Identification of Genes Differentially Expressed in Responseto Paradigm C: IL-1 Induction of Endothelial Cells

According to the invention, differential display was used to detect fournovel genes that are differentially expressed in endothelial cells thatwere treated in vitro with IL-1. Three of these genes, rchd024, rchd032,and rchd036, are not homologous to any known gene. The fourth gene,rchd005, is 70% homologous to a cloned shark gene calledbumetanide-sensitive Na-K-Cl cotransport protein. A human homolog ofthis gene has been reported, but the sequence has not yet been published(Xu et al., 1994, Proc. Natl. Acad. Sci. USA 91: 2201-2205). Thediscovery of the up-regulation of these four genes provides afingerprint profile of IL-1 induced endothelial cells. This fingerprintprofile can be used in the treatment and diagnosis of cardiovasculardiseases, including but not limited to atherosclerosis,ischemia/reperfusion, hypertension, restenosis, and arterialinflammation.

8.1. MATERIALS AND METHODS

Primary cultures of HUVEC's were established from normal term umbilicalcords as described (In Progress in Hemostasis and Thrombosis, Vol. 3, P.Spaet, editor, Grune & Stratton Inc., New York, 1-28). Cells were grownin 20% fetal calf serum complete media (Luscinskas et al., 1989, J.Immunol. 142: 2257-2263) and passaged 1-3 times before activation.

For activation, cells were cultured with 10 units/ml of human IL-1β for1 or 6 hr. before lysis in guanidinium isothiocyanate RNA lysis buffer(Sambrook et al., 1989, supra). Lysed cells were then syringed with a 23G. needle, layered over 5.7M CsCl, and centrifuged for 20 hr. at 35 K.

Alternatively, cells were induced in the presence of 100 μMlysophosphatidylcholine, or 50 μg/ml oxidized human LDL (Sigma) forperiods of 1 or 6 hr. RNA was isolated as described, above, in Section6.1. Differential display, Northern analysis, RT-PCR, subcloning, andDNA sequencing were carried out as described, above, in Section 6.1.2,except that Northern blot hybridizations were carried out as follows:for pre-hybridization, the blot was placed into roller bottle containing10 ml of rapid-hyb solution (Amersham), and placed into 65° C. incubatorfor at least 1 hr. For hybridization, 1×10⁷ cpm of the probe was thenheated to 95° C., chilled on ice, and added to 10 ml of rapid-hybsolution. The prehybridization solution was then replaced with probesolution and incubated for 3 hr at 65° C. The following day, the blotwas washed once for 20 min. at r.t. in 2x SSC/0.1% SDS and twice for 15min. at 65° C. in 0.1x SSC/0.1% SDS before being covered in plastic wrapand put down for exposure.

Chromosomal locations were determined according to the method describedin Section 6.1.3, above. For rchd024, the primers used werefor-cccatagactaggctcatag, and rev-tttaaagagaaattcaaatc.

8.2. RESULTS

HUVEC's were activated with 10 units/ml IL-1β for 1 or 6 hours andcompared to resting HUVEC's using differential display. As shown in FIG.5, a band marked rchd005 is present in lanes 11 and 12 (IL-1, 6 hr.) butnot in lanes 9 and 10 (control), or lanes 7 and 8 (IL-1, 1 hr.). Thisband, rchd005, was isolated and subcloned and sequenced. When a probeprepared form this band was used to screen a Northern blot, expressionwas seen at 6 hr., but not at 1 hr. or in the control (FIG. 6). However,when this same probe was hybridized to a Northern blot prepared fromshear stressed RNA, according to Paradigm D described in Section 9,below, a different pattern of up-regulation was also seen (FIG. 7).Expression was up at 1 hr. and then nearly disappeared by 6 hr.Amplified rchd005 DNA was subcloned and sequenced. Sequence analysisrevealed an approximately 360 bp insert (FIG. 8) with 70% sequencesimilarity to a cloned shark gene called bumetanide-sensitive Na-K-Clcotransport protein.

Another IL-1 inducible band, rchd024, is shown in FIG. 9. Northernanalysis on IL-1 up-regulated RNA reveals a 10 kb message present at 6hr. (FIG. 10) that also shows a low level of up-regulation under shearstress at 6 hr. (FIG. 11). The DNA sequence was obtained from subclonesof amplified DNA (FIG. 12). Database searching revealed no significantsequence similarities. A PCR amplification experiment determined thatthe rchd024 gene is located on human chromosome 4.

Band rchd032 was isolated on the basis of its differentially increasedexpression after 6 hr. treatment with IL-1 (FIG. 13), which wasconfirmed by RT-PCR analysis (FIG. 14). Amplified rchd032 sequences weresubcloned and sequenced (FIG. 15). No significant homology to any knowngene was found.

Band rchd036 was also isolated on the basis of its differentialexpression 6 hr. after IL-1 treatment (FIG. 16). Northern analysis (FIG.17) revealed an 8 kb band which was up-regulated 6 hr. after IL-1treatment. Another Northern analysis was performed testing rchd036 underthe shear stress condition of Paradigm D, which are described in theexample in Section 9, below. Interestingly, rchd036 is not induced byshear stress, as indicated by the lack of any band after either 1 hr. or6 hr. of treatment (FIG. 33). This result provides an example of anIL-1-inducible endothelial cell gene that is not regulated by shearstress, indicating that these induction pathways can be separated, andmay provide for drugs with greater specificity for the treatment ofinflammation and atherosclerosis. The DNA sequence was obtained fromsubclones of amplified DNA (FIG. 18), and a search of the databaserevealed no sequence similarities. A PCR amplification experimentdetermined that the rchd036 gene is located on human chromosome 15.

9. EXAMPLE Identification of Genes Differentially Expressed in Responseto Paradigm D: Endothelial Cell Shear Stress

According to the invention, differential display was used to detectgenes that are differentially expressed in endothelial cells that weresubjected to fluid shear stress in vitro. Shear stress is thought to beresponsible for the prevalence of atherosclerotic lesions in areas ofunusual circulatory flow. Using the method of Paradigm D, four bandswith novel DNA sequences were identified.

rchd528 does not share homology with any known gene. rchd502, on theother hand is homologous to rat matrin F/G mRNA sequence. This rat geneencodes a protein that is found in the nuclear matrix and contains thezinc finger DNA binding motif, (Hakes, et al., 1991, Proc. Natl. Acad.Sci. U.S.A. 88:6186-6190). In fact, the sequences in rchd502 encode partof the zinc finger portion of the protein. Given that rchd502 isup-regulated by a mechanical force and the rat matrin protein is anuclear structural protein that also binds to DNA, rchd502 may beinvolved in translating a physical force on the cell into a program ofgene expression. Furthermore, rchd502 is first gene demonstrated to beup-regulated by shear-stress but not by IL-1. It therefore provides anexcellent novel tool for diagnosis and treatment of cardiovasculardisease.

The complete sequence of the rchd523 gene reveals that it encodes anovel G protein-coupled receptor protein, consisting of 375 amino acidsand a multiple transmembrane domain sequence motif. The discovery ofsuch a novel protein is particularly useful in designing treatments aswell as diagnostic and monitoring systems for cardiovascular disease. Incarrying out signal transduction, G proteins play an important earlyrole in the pathways that cause changes in cellular physiology. Therchd523 gene product, therefore, provides an excellent target forintervention in the treatment of cardiovascular disease. Furthermore, asa transmembrane protein, the rchd523 gene product can be readilyaccessed (e.g., by inhibitory compounds during treatment) or detected onthe endothelial cell surface. It, therefore, also provides an excellenttarget for detection of cardiovascular disease states in diagnosticsystems, as well as in the monitoring of the efficacy of compounds inclinical trials. Furthermore, the extracellular domains of the rchd523gene product provide especially efficient screening systems foridentifying compounds that bind to the rchd523 gene product. Suchcompounds can be useful in treating cardiovascular disease by inhibitingrchd523 gene product activity.

The sequence of the complete coding region of the rchd534 gene was alsoobtained. The rchd534 gene encodes a novel protein consisting of 235amino acids.

Also using the method of Paradigm D, the previously identified humanprostaglandin endoperoxide synthase type II was isolated. This gene waspreviously known to be involved in inflammation, and to be up-regulatedby IL-1 (Jones et al., 1993, J. Biol. Chem. 268: 9049-9054), but itsup-regulation by shear stress was previously unknown. This resultconfirmed the general effectiveness of the techniques used according tothe invention in the detection of genes involved cardiovascular disease.

Furthermore, the up-regulation of these five genes in shear stressedendothelial cells provides a fingerprint for the study of cardiovasculardiseases, including but not limited to atherosclerosis,ischemia/reperfusion, hypertension, and restenosis. The fact that one ofthese genes, rchd502, is not up-regulated under Paradigm C (IL-1induction) provides an extremely useful means of distinguishing andtargeting physiological phenomena specific to shear stress.

9.1. MATERIALS AND METHODS

Primary cultures of HUVEC's were established from normal term umbilicalcords as described (In Progress in Hemostasis and Thrombosis, Vol. 3, P.Spaet, editor, Grune & Stratton Inc., New York, 1-28). Cells were grownin 20% fetal calf serum complete media (1989, J. Immunol. 142:2257-2263) and passaged 1-3 times before shear stress induction.

For induction, second passage HUVEC's were plated on tissueculture-treated polystyrene and subjected to 10 dyn/cm2 laminar flow for1 and 6 hr. as described (Nagel et al., 1994, J. Clin. Invest. 94:885-891) or 3-10 dyn/cm² turbulent flow as previously described (Davieset al., 1986 Proc. Natl. Acad. Sci. U.S.A. 83: 2114-2117). RNA wasisolated as described, above, in Section 6.1. Differential display,Northern analysis, RT-PCR, subcloning, and DNA sequencing were carriedout as described, above, in Section 6.1.2, except that Northern blothybridizations were carried out as described, above, in Section 8.1.

For rchd523, the RACE procedure kit was used to obtain the entire codingregion of the rchd523 gene. The procedure was carried out according tothe manufacturer's instructions (Clonetech, Palo Alto, Calif.; see also:Chenchik, et al., 1995, CLONTECHniques (X) 1: 5-8; Barnes, 1994, Proc.Natl. Acad. Sci. USA 91: 2216-2220; and Cheng et al., Proc. Natl. Acad.Sci. USA 91: 5695-5699). Primers were designed based on amplifiedrchd523 sequences. Template mRNA was isolated from shear stressedHUVEC's.

For rchd534, amplified sequences, which contained a portion of the gene,were subcloned and then used to retrieve the entire coding region of therchd534 gene. Probes were prepared by isolating the subcloned insert DNAfrom vector DNA, and labeling with ³²P as described above in Section6.1.2. Labeled insert DNA was used to probe a cDNA library, preparedfrom mRNA which was isolated from shear stressed HUVEC's as described inthis section, above. The cDNA library was produced and screenedaccording to well-known methods (Sambrook et al., 1989, supra), usingthe bacteriophage λ-ZAP vector (Stratagene, LaJolla, Calif.). Plaquesthat were detected by the rchd534 probe were isolated and sequenced.

Determination of chromosomal location was carried out according to themethod described in Section 6.1.3, above. The primers used for rchd523were (for-atgccgtgtgggttagtc) and (rev-attttatgggaaggtttttaca); and forrchd534 were (for-cttttctgcgtctcccat) and (rev-agacatcagaaactccaacc).

9.2. RESULTS

HUVEC's were subjected to laminar shear stress for 1 or 6 hr. andcompared to static control cells in differential display. As shown inFIG. 19, a band (rchd502) is identified which is found in lanes 5,6 (6hr.) but not in lanes 1,2 (control). This band was excised, amplified,and sequenced. Northern analysis using amplified rchd502 sequencesrevealed a 4.5 kb band that is up-regulated at 6 hr. compared tocontrols (FIG. 20). When rchd502 probe was hybridized to a Northern blotprepared from IL-1 induced endothelial cells, up-regulation of a 4.5 kbband is not seen (FIG. 21). This result provides the first example of ashear stress-inducible endothelial cell gene that is not regulated byIL-1, indicating that these induction pathways can be separated, and mayprovide for drugs with greater specificity for the treatment ofinflammation and atherosclerosis. Sequencing was done, and the resultingsequence is shown in FIG. 22. When this sequence was compared to thesequence database, an 84% (183/217) sequence similarity with Rat matrinF/G mRNA sequence was obtained.

Shear stress band rchd505 decreased 1 hr. and 6 hr. after shear stress,as compared to untreated control cells (FIG. 23). Northern analysisrevealed differential expression except that rchd505 was up-regulatedafter 1 hr. and 6 hr. shear stress treatment (FIG. 24). This same bandwas similarly up-regulated in cells treated with IL-1 according toParadigm C (FIG. 25). Sequence analysis revealed that rchd505 is thepreviously characterized human endoperoxide synthase type II.

rchd523 was detected under differential display as a band up-regulatedafter 1 hr. and 6 hr. shear stress treatment (FIG. 26). The 6 hr.up-regulation of rchd523 was confirmed by RT-PCR using rchd523 primersfor-atgccgtgtgggttagtc (SEQ ID NO:28)/rev-attttatgggaaggtttttaca (SEQ IDNO:29) and human actin control primers for-accctgaagtaccccat (SEQ IDNO:16)/rev-tagaagcatttgcggtg (SEQ ID NO:17). Amplified rchd523 sequenceswere subcloned, and an isolate was sequenced and designated pRCHD523.The RACE procedure was used to obtain a 2.5 kb cDNA containing theentire coding sequence of the rchd523 gene. The cDNA isolate containingthe complete coding sequence of rchd523 is designated pFCHD523. Sequenceanalysis revealed that the rchd523 gene product encodes a novel Gprotein-coupled receptor, consisting of 375 amino acids and a multipletransmembrane domain sequence motif. A PCR amplification experimentdetermined that the rchd523 gene is located on human chromosome 7.

rchd528 was also detected as an up-regulated band after 1 hr. and 6 hr.shear stress treatment (FIG. 28). This result was confirmed by Northernanalysis in which probes of rchd528 amplified sequence detected anapproximately 5.0 kb message that was up-regulated moderately after 1hr., and up-regulated very strongly after 6 hr. (FIG. 29). The amplifiedsequences were subcloned and sequenced (FIG. 30A-K). Comparison withsequences in the database revealed no homologies between rchd528 and anyknown DNA sequence.

rchd534 also was detected as being up-regulated in response to shearstress. Northern analysis revealed that rchd534 is strongly inducedafter 6 hours of shear stress treatment (FIG. 33). The amplifiedsequences were subcloned, sequenced, and re-isolated for use as a probefor retrieving full-length rchd534 cDNA. A 3.3 kb λ-ZAP clone wassequenced to reveal full-length rchd534 cDNA (FIGS. 34A-D). This clonecontaining the entire coding region the rchd534 gene was designatedpFCHD534. The encoded protein consists of 235 amino acids. Comparisonwith sequences in the database revealed no homologies between rchd534and any known DNA sequences. A PCR amplification experiment determinedthat the rchd534 gene is located on human chromosome 15. rchd534 wasalso shown not to be regulated by IL-1 when tested under the conditionsof Paradigm C, as described in Section 8, above. Just like rchd502,rchd534 is an example of a shear stress-inducible endothelial cell genethat is not regulated by IL-1, confirming that these induction pathwayscan be separated, and may provide for drugs with greater specificity forthe treatment of inflammation and atherosclerosis.

10. EXAMPLE Use of Genes Under Paradigm A as Surrogate Markers inClincial Trails

According to the invention, the fingerprint profile derived from any ofthe paradigms described in Sections 5.1.1.1 through 5.1.1.6 may be usedto monitor clinical trials of drugs in human patients. The fingerprintprofile, described generally in Section 5.5.4, above, indicates thecharacteristic pattern of differential gene regulation corresponding toa particular disease state. Paradigm A, described in Section 5.1.1.1,and illustrated in the example in Section 6, above, for example,provides the fingerprint profile of monocytes under oxidative stress.This profile gives an indicative reading, therefore, of thephysiological response of monocytes to the uptake of oxidized LDL.Accordingly, the influence of anti-oxidant drugs on the oxidativepotential may be measured by performing differential display on themonocytes of patients undergoing clinical tests.

10.1. TREATMENT OF PATIENTS AND CELL ISOLATION

Test patients may be administered compounds suspected of havinganti-oxidant activity. Control patients may be given a placebo.

Blood may be drawn from each patient after a 12 hour period of fastingand monocytes may be purified as described, above, in Section 7.1.1. RNAmay be isolated as described in Section 6.1.1, above.

10.2. ANALYSIS OF SAMPLES

RNA may be subjected to differential display analysis as described inSection 6.1.2, above. A decrease in the physiological response state ofthe monocytes is indicated by a decreased intensity of those bands thatwere up-regulated by oxidized LDL under Paradigm A, and an increasedintensity of those bands that were down-regulated by oxidized LDL underParadigm A, as described in Section 6.2, above.

11. EXAMPLE Imaging of a Cardiovascular Disease Condition

According to the invention, differentially expressed gene products whichare localized on the surface of affected tissue may be used as markersfor imaging the diseased or damaged tissue. Conjugated antibodies thatare specific to the differentially expressed gene product may beadministered to a patient or a test animal intravenously. This methodprovides the advantage of allowing the diseased or damaged tissue to bevisualized non-invasively.

11.1. MONOCLONAL CONJUGATED ANTIBODIES

The differentially expressed surface gene product, such as the rchd523gene product, is expressed in a recombinant host and purified usingmethods described in Section 5.4.2, above. Preferably, a proteinfragment comprising one or more of the extracellular domains of therchd523 product is produced. Once purified, it is be used to produceF(ab′)₂ or Fab fragments, as described in Section 5.4.3, above. Thesefragments are then labelled with technetium-99m (^(99m)Tc) using aconjugated metal chelator, such as DTPA as described in section 5.8.3,above.

11.2. ADMINISTRATION AND DETECTION OF IMAGING AGENTS

Labeled MAb may be administered intravenously to a patient beingdiagnosed for atherosclerosis, restenosis, or ischemia/reperfusion.Sufficient time is allowed for the detectably-labeled antibody tolocalize at the diseased or damaged tissue site (or sites), and bind tothe rchd523 gene product. The signal generated by the label is detectedby a photoscanning device. The detected signal is then converted to animage of the tissue, revealing cells, such as endothelial cells, inwhich rchd523 gene expression is up-regulated.

12. EXAMPLE Screening for Ligands of the rchd 523 Gene Product andAntagonists of rchd523 Gene Product-Ligand Interaction

The rchd523 gene product is a member of the G protein-coupled receptorprotein family, containing multiple transmembrane domains. The receptorbinding activity of this protein family is detected by assaying for Ca²⁺mobility through the membrane of cells in which the receptor gene isexpressed. This assay, described below, is used to identify ligands thatbind to the rchd523 gene product receptor. Establishing thisligand-receptor activity then provides for a screen in which antagonistsof the ligand-receptor interaction are identified. An antagonist isdetected by its ability to inhibit the Ca²⁺ mobility induced byligand-receptor binding. Such antagonists, therefore, provide compoundsthat are useful in the treatment of cardiovascular disease, bycounteracting the activity of the product of this target gene which isup-regulated in the disease state.

Binding of ligand to the rchd523 gene product is measured as follows.The cDNA containing the entire coding region of the rchd523 gene isremoved from pFCHD523 and placed under the control of a promoter that ishighly expressed in mammalian cells in an appropriate expression vector.The resulting construct is transfected into myeloma cells, which arethen loaded with FURA-2 or INDO-1 by standard techniques. Ligands areadded to the cell culture to test their ability to bind to the rchd523receptor in a manner that triggers signal transduction, as measured byCa²⁺ mobilization across the cell membrane. Mobilization of Ca²⁺ inducedby ligand is measured by fluorescence spectroscopy as described inGrynkiewicz et al., 1985, J. Biol. Chem. 260:3440. Ligands that reactwith the target gene product receptor domain are identified by theirability to produce a fluorescent signal. Their receptor bindingactivities are quantified and compared by measuring the level offluorescence produced over background.

Candidate antagonists are then screened for their ability to interferewith ligand-receptor binding. Myeloma transfectants expressing rchd523gene product are treated with ligand alone, and ligand in the presenceof candidate antagonist. Candidate antagonists that cause a reduction inthe fluorescence signal are designated antagonists of the ligand-rchd523receptor interaction.

13. DEPOSIT OF MICROORGANISMS

The following microorganisms were deposited with the AgriculturalResearch Service Culture Collection (NRRL), Peoria, Ill., on Jan. 11,1995 and assigned the indicated accession numbers:

Microorganism NRRL Accession No. RCHD005 B-21376 RCHD024 B-21377 RCHD032B-21378 RCHD036 B-21379 RCHD502 B-21380 RCHD523 B-21381 RCHD528 B-21382

The following microorganisms were deposited with the AgriculturalResearch Service Culture Collection (NRRL), Peoria, Ill., on Jun. 6,1995 and assigned the indicated accession numbers:

Microorganism NRRL Accession No. FCHD523 B-21458 FCHD534 B-21459

The present invention is not to be limited in scope by the specificembodiments described herein, which are intended as single illustrationsof individual aspects of the invention, and functionally equivalentmethods and components are within the scope of the invention. Indeed,various modifications of the invention, in addition to those shown anddescribed herein will become apparent to those skilled in the art fromthe foregoing description and accompanying drawings. Such modificationsare intended to fall within the scope of the appended claims.

38 288 base pairs nucleic acid both unknown cDNA NO unknown 1 GGCTTAGATGCAGCCTGCAA ATTAAACTTT GATTTTTCAT CTTGTGAAAG CAGTCCTTGT 60 TCCTATGGCCTAATGAACAA CTTCCAGGTA ATGAGTATGG TGTCAGGATT TACACCACTA 120 ATTTCTGCAGGTATATTTTC AGCCACTCTT TCTTCAGCAT TAGCATCCCT AGTGAGTGCT 180 CCCAAAATATTTCAGGCTCT ATGTAAGGAC AACATCTACC CAGCTTTCCA GATGTTTGCT 240 AAAGGTTATGGGAAAAATAA TGAACCTCTT CGTGGCTGCA TCTAAGCC 288 178 base pairs nucleicacid both unknown cDNA NO unknown 2 AAAAATAAAT AAATTAAAGT CTGAGACCAATTTGCCACTG TGAATATAAG CACATTAACC 60 CCAGGAGGAG CCAAGAACTA CACAAACCTCTCTATGAGAA TTTACCAGTC TTCTTTCATT 120 TGGCAAGAAA AAGCTCAGGA AAATTTGCTTGTTTAAATTC TATGAGCCTA GTCTATGG 178 101 base pairs nucleic acid bothunknown cDNA NO unknown 3 GGGTAATTCA TTAATTACAC TTTAAAATTG GAAAGTGGGATAAGAAATCT AAAGTAAACC 60 AGCTTATCTT TGAAACAATA TTATTTTGAA ATTGGCTTTA A101 184 base pairs nucleic acid both unknown cDNA NO unknown 4GGCTTGGTGG TGATGCCTAC AAGAAATGTT TACATACAAA CACTCTATAC ATCTAACTCC 60CGAAAAAGGA CCAGCTATTT CGGCAACAGA AAAAAGACAA GCATTTCAGA GGAGCGTTGC 120TTTCCTTAAA GACCTAACTC ACTTAAGTCT TACAAACAGA AATAACAAGG AGGACAATTT 180TCTA 184 284 base pairs nucleic acid both unknown cDNA NO unknown 5CTTGGGGATG CTGTTTGGAG GAATCCTCAT GAAGCGCTTT GTTTTCTCTC TACAAGCCAT 60TCCCCGCATA GCTACCACCA TCATCACCAT CTCCATGATC CTTTGTGTTC CTTTGTTCTT 120CATGGGATGC TCCACCCCAA CTGTGGCCGA AGTCTACCCC CCTAGCACAT CAAGTTCTAT 180ACATCCGCAG TCTCCTGCCT GCCGCAGGGA CTGCTCGTGC CCAGATTCTA TCTTCCACCC 240GGTCTGTGGA GACAATGGAA TCGAGTACCT CTCCCCTTGC CATG 284 2582 base pairsnucleic acid both unknown cDNA NO unknown 6 GGCTTACCAT CGATGCGGCCGCGGATCCAG GGCTCAGAGG GAGGACGCAC CCGCCAGCCA 60 GCCGGGAACC TTCCCTCGCGGGCTCCCAGG GCGGGTCTCT TCCTCTCTCT AGCCCTGCTC 120 AGGCATTCGG CAGGTCCAGCAGAGGTACAC CTCCTGCAGC GGGTTCCAAG TGCACCTCCA 180 GCCTGATGGA CCTGACCAAGGAGGCTTCCA GGAGCACAGA AGGGGCTGCA ACCCAGGTAC 240 CCAGAGAGTG AGCAGCTCCACGCGGGACTG TGCACGGTGG CCGACACCCG CAGGGACGCC 300 CACCGGACGA GCACGCGGAGGGCCCTCGCC TCCACGGATG CACCATGCCG GTGTGAGGAG 360 CATCTGTTCT TCCCACTCTCTGCAGTTAAC AAACCCAACC CAAACCACCA CAGGTGCTCC 420 TCCTGGGGAG TTTCCTGTCTGACAAATGCC AGGCTCACTT CAAGGAGAAT CACGCTTCTT 480 TCTAAAGATG GATTCACCATTTAAAACAGA GCTCTGGGAG CCTTTCGGCA AATCTTGAAA 540 GCTGCACGGC GCAGAGACATGGATGTGACT TCCCAAGCCC GGGGCGTAGG CCTGGAGATG 600 TACCCAGGCA CCGCGCAGCCTGCGGCCCCC AACACCACCT CCCCCGAGCT CAACCTGTCC 660 CACCCGCTCC TGGGCACCGCCCTGGCCAAT GGGACAGGTG AGCTCTCGGA GCACCAGCAA 720 TACGTGATCG GCCTGTTCCTCTCGTGCCTC TACACCATCT TCCTCTTCCC CATCGGCTTT 780 GTGGGCAACA TCCTGATCCTGGTGGTGAAC ATCAGCTTCC GCGAGAAGAT GACCATCCCC 840 GACCTGTACT TCATCAACCTGGCGGTGGCG GACCTCATCC TGGTGGCCGA CTCCCTCATT 900 GAGGTGTTCA ACCTGCACGAGCGGTACTAC GACATCGCCG TCCTGTGCAC CTTCATGTCG 960 CTCTTCCTGC GGGTCAACATGTACAGCAGC GTCTTCTTCC TCACCTGGAT GAGCTTCGAC 1020 CGCTACATCG CCCTGGCCAGGGCCATGCGC TGCAGCCTGT TCCGCACCAA GCACCACGCC 1080 CGGCTGAGCT GTGGCCTCATCTGGATGGCA TCCGTGTCAG CCACGCTGGT GCCCTTCACC 1140 GCCGTGCACC TGCAGCACACCGACGAGGCC TGCTTCTGTT TCGCGGATGT CCGGGAGGTG 1200 CAGTGGCTCG AGGTCACGCTGGGCTTCATC GTGCCCTTCG CCATCATCGG CCTGTGCTAC 1260 TCCCTCATTG TCCGGGTGCTGGTCAGGGCG CACCGGCACC GTGGGCTGCG GCCCCGGCGG 1320 CAGAAGGCGC TCCGCATGATCCTCGCAGTG GTGCTGGTCT TCTTCGTCTG CTGGCTGCCG 1380 GAGAACGTCT TCATCAGCGTGCACCTCCTG CAGCGGACGC AGCCTGGGGC CGCTCCTTGC 1440 AAGCAGTCTT TCCGCCATGCCCACCCCCTC ACGGGCCACA TTGTCAACCT CGCCGCCTTC 1500 TCCAACAGCT GCCTAAACCCCCTCATCTAC AGCTTTCTCG GGGAGACCTT CAGGGACAAG 1560 CTGAGGCTGT ACATTGAGCAGAAAACAAAT TTGCCGGCCC TGGACCGCTT CTGTCACGCT 1620 GCCCTGAAGG CCGTCATTCCAGACAGCACC GAGCAGTCGG ATGTGAGGTT CAGCAGTGCC 1680 GTGTAGACAG CCTTGGCCGCATAGGCCCAG CCAGGGTGTG ACTCGGGAGC TGCACACACC 1740 TGGGTGGACA CAAGGCACGGCCACGTCATG TCTCTAAACT GCGGTCAGAT GTGGCTTCTG 1800 GCTCCTCGGG CCTCGCGAGGGTCACGCTTG CCTGGTCACC CTGGGGCTGC TTAGGAAACC 1860 TCAGGACTGG TCACCTTGCACTCCTCACAC AGAATTGCTA CAATCCCAAA GCGCTCGCCC 1920 CGCAGGGTCC AAAGGCCAGCGGTGACCAGC CTGTCACCCA GCTCCTCCCC GCCAACCCTG 1980 CCTGCCGCTG CACCTGCCCGCTGCTGCAGG AAACATTTCT GACACCGTCG ACCAGGAAAG 2040 CCACACGGAG AGGCCACTGTGGGTGAAGCG CCTCAGTTAC ACAGGAACCC TAAAGCAAAT 2100 CTGCCACCGT GGGGGAACTGACGCTGGAGA TGCAAGGTGC TGGTGGGTCT GAGCTGGACG 2160 TCGCGGTGTG TCCTCTGTGCCCACGGTCTG AGCTAGCTAG CGCACCGCCG AGTTAAAGAG 2220 GAGAAGGAAA ACATGCTGCTCTGGTGCACG CCTGAGCGTC CTCCATCTTC CAGGATGGCA 2280 GCAATGGCGC TGTGCGGCCTCACCAGGCCC ACGAGGAGCA GCAGCGCTCG GCCCGGAGCA 2340 GCAGGAAGGC CCCTCTGTGGAGCGCCCGCC GTCTGCTCCG GGGTGGTTCA GTCACTGCTT 2400 GTTGACATCA ACATGGCAATTGCACTCATG TGGACTGGGA CCGTGCGAGC TGCCGTGTGG 2460 GTTAGTCGGG TGCCAGGACAATGAAATACT CCAGCACCTG TGGCTGACGA ATTCGTTTCT 2520 ACAGAAGTAA CAGCTGGGGACAACTGCGAT GATGATGTAA AAACCTTCCC ATAAAATAAG 2580 CC 2582 128 base pairsnucleic acid both unknown cDNA NO unknown 7 GGGAGGTGGG CTCCTGCTCATCCTAGGCAT CGCACTGATT GTTACCTGTT GCAGAAAGAA 60 TAAAAATGAC ATAAGCAAACTCATCTTCAA AAGTGGAGAT TTCCAAATGT CCCCGTATGC 120 TGAATACC 128 13 basepairs nucleic acid single linear DNA (genomic) NO unknown misc_feature12 8 TTTTTTTTTT TNG 13 10 base pairs nucleic acid single linear DNA(genomic) NO unknown 9 AGCATGGCTC 10 23 base pairs nucleic acid singlelinear DNA (genomic) NO unknown 10 CACCCCTGGC ATCTTCTCCT TCC 23 24 basepairs nucleic acid single linear DNA (genomic) NO unknown 11 ATCCTCCCCCAGTTCACCCC ATCC 24 21 base pairs nucleic acid single linear DNA(genomic) NO unknown 12 CCTGATAGAT GGGCACTGTG T 21 22 base pairs nucleicacid single linear DNA (genomic) NO unknown 13 GAACACGGCA TTGTCACTAA CT22 22 base pairs nucleic acid single linear DNA (genomic) NO unknown 14AAGTCGCGCC CGCCCCTGAA AT 22 24 base pairs nucleic acid single linear DNA(genomic) NO unknown 15 GATCCCTGGC CACCGTCCGT CTGA 24 17 base pairsnucleic acid single linear DNA (genomic) NO unknown 16 ACCCTGAAGTACCCCAT 17 17 base pairs nucleic acid single linear DNA (genomic) NOunknown 17 TAGAAGCATT TGCGGTG 17 10 base pairs nucleic acid singlelinear DNA (genomic) NO unknown 18 AGATGCAGCC 10 13 base pairs nucleicacid single linear DNA (genomic) NO unknown misc_feature 12 19TTTTTTTTTT TNA 13 10 base pairs nucleic acid single linear DNA (genomic)NO unknown 20 TCTCCCTCAG 10 13 base pairs nucleic acid single linear DNA(genomic) NO unknown misc_feature 12 21 TTTTTTTTTT TNC 13 10 base pairsnucleic acid single linear DNA (genomic) NO unknown 22 TGGAGAGCAG 10 23base pairs nucleic acid single linear DNA (genomic) NO unknown 23ATTTATAAAG GGGTAATTCA TTA 23 22 base pairs nucleic acid single linearDNA (genomic) NO unknown 24 TTAAAGCCAA TTTCAAAATA AT 22 10 base pairsnucleic acid single linear DNA (genomic) NO unknown 25 GGTGGTGATG 10 10base pairs nucleic acid single linear DNA (genomic) NO unknown 26GGTGCGGGAA 10 10 base pairs nucleic acid single linear DNA (genomic) NOunknown 27 ACATGCCGTG 10 18 base pairs nucleic acid single linear DNA(genomic) NO unknown 28 ATGCCGTGTG GGTTAGTC 18 22 base pairs nucleicacid single linear DNA (genomic) NO unknown 29 ATTTTATGGG AAGGTTTTTA CA22 10 base pairs nucleic acid single linear DNA (genomic) NO unknown 30AATGCGGGAG 10 13 base pairs nucleic acid single linear DNA (genomic) NOunknown misc_feature 12..13 31 TTTTTTTTTT TNN 13 13 base pairs nucleicacid single linear DNA (genomic) NO unknown 32 TTTTTTTTTT TCC 13 10 basepairs nucleic acid single linear DNA (genomic) NO unknown 33 GTGACATGCC10 20 base pairs nucleic acid single linear DNA (genomic) NO unknown 34CATGCCTGTA GAAAAAGGTT 20 20 base pairs nucleic acid single linear DNA(genomic) NO unknown 35 CTTCATAGAA TCTAAGCCTA 20 3083 base pairs nucleicacid both unknown cDNA unknown misc_feature 16 misc_feature 30misc_feature 2911 36 GAATTCGGCA CGAGGMCAGG AGCTCCTTTW CTGCGTCTCCCATCATGGGG CTTAGGGTTG 60 AGTCTTCAGG TTCTGGGGGC AGGAAGGACG GGCACTCAGGAGGCCCCCTC CCCATCCACA 120 GCCCCTCTTT GGGAGGGGGG AAACTTGGCA ACCCGGGAGGCATGTGGATC TTTTCCTAAG 180 CAAGATGCTG AGCTGGAAAG ATGGGGGTGT AAGGTAATGTCCCAAACTGA AACTTTGCCA 240 GGCACTGGGA GAGGCTGTGA ACTCTTTTCT GGCTTTAGAATTTAGGTCTA GATCCCAAAA 300 GGCTAAGTAC CCCCTGGGGG CTAACCAGAG GCATGCCTGGGCTGAGCTGA ACCTTCTGGT 360 GCACTGGCCC CTGGCTGACT GCTCTTCTGC AGGAAGTTGGAGGAGATTCC TGAAGTTGAT 420 TCCTCAGGCT GGATGTCCAA GGGGGTTGGA GTTTCTGATGTCTTTCTGTC TCCCTCTCTT 480 TTCTTTCTCT CCCTACCAGG TCCACTTCTT TCAGAGGGGCCTGCGGTGCT CTAAAAGTTC 540 TCCTGTTAAA GTTTAGAGCA AATTGGTTAT TATTTTAAAATCAATAAAAC TTTTAAAAGT 600 ACTAAGACAA CTTCTAAGAG GGGAGTGGAC AGAGGGCCTGGTGGCAGCTC ACAGTTTCTT 660 TTCTGACCTT TGGTCTCACC CACCAAGTGT CCCACCTGAGTGCCCACCTT GCCCACCTGA 720 GGTAATGCCC TGGGGCTCCA CCAGTCCAGA TCCACAGGGCGCAGCCATGT GGGAGTGGCG 780 GCTGATTGTT ACCCAGTAGT GTTGATAGCA CATTATTCATAACAGCCAAA GAGAGGAAGC 840 AACCCAAATG TCCATTAGCT GATAAATGGA TAAATGAAATATGGTACGTC CGAAGAATGG 900 AATATCATTC ACCCATGAAA AAGAACGAAG TCCAGCACCAAAACGTGCTA CAACATGGAT 960 GAACTTCGAT GACTTTGTGC CACATGAAAG AAGAAGCCAGCCACAAAAGG CCATATATTG 1020 TATGAAATGA AATGTCCAGA ATGGGCAAAC CCATAGAGACACAAAAATCT CCGCCACCTC 1080 CCTACTCTCG GCTGTCTCCT CGCGACGAGT ACAAGCCACTGGATCTGTCC GATTCCACAT 1140 TGTCTTACAC TGAAACGGAG GCTACCAACT CCCTCATCACTGCTCCGGGT GAATTCTCAG 1200 ACGCCAGCAT GTCTCCGGAC GCCACCAAGC CGAGCCACTGGTGCAGCGTG GCGTACTGGG 1260 AGCACCGGAC GCGCGTGGGC CGCCTCTATG CGGTGTACGACCAGGCCGTC AGCATCTTCT 1320 ACGACCTACC TCAGGGCAGC GGCTTCTGCC TGGGCCAGCTCAACCTGGAG CAGCGCAGCG 1380 AGTCGGTGCG GCGAACGCGC AGCAAGATCG GCTTCGGCATCCTGCTCAGC AAGGAGCCCG 1440 ACGGCGTGTG GGCCTACAAC CGCGGCGAGC ACCCCATCTTCGTCAACTCC CCGACGCTGG 1500 ACGCGCCCGG CGGCCGCGCC CTGGTCGTGC GCAAGGTGCCCCCCGGCTAC TCCATCAAGG 1560 TGTTCGACTT CGAGCGCTCG GGCCTGCAGC ACGCGCCCGAGCCCGACGCC GCCGACGGCC 1620 CCTACGACCC CAACAGCGTC CGCATCAGCT TCGCCAAGGGCTGGGGGCCC TGCTACTCCC 1680 GGCAGTTCAT CACCTCCTGC CCCTGCTGGC TGGAGATCCTCCTCAACAAC CCCAGATAGT 1740 GGCGGCCCCG GCGGGAGGGG CGGGTGGGAG GCCGCGGCCACCGCCACCTG CCGGCCTCGA 1800 GAGGGGCCGA TGCCCAGAGA CACAGCCCCC ACGGACAAAACCCCCCAGAT ATCATCTACC 1860 TAGATTTAAT ATAAAGTTTT ATATATTATA TGGAAATATATATTATACTT GTAATTATGG 1920 AGTCATTTTT ACAATGTAAT TATTTATGTA TGGTGCAATGTGTGTATATG GACAAAACAA 1980 GAAAGACGCA CTTTGGCTTA TAATTCTTTC AATACAGATATATTTTCTTT CTCTTCCTCC 2040 TTCCTCTTCC TTACTTTTTA TATATATATA TAAAGAAAATGATACAGCAG AGCTAGGTGG 2100 AAAAGCCTGG GTTTGGTGTA TGGTTTTTGA GATATTAATGCCCAGACAAA AAGCTAATAC 2160 CAGTCACTCG ATAATAAAGT ATTCGCATTA TAGTTTTTTTTAAACTGTCT TCTTTTTACA 2220 AAGAGGGGCA GGTAGGGCTT CAGCGGATTT CTGACCCATCATGTACCTTG AAACTTGACC 2280 TCAGTTTTCA AGTTTTACTT TTATTGGATA AAGACAGAACAAATTGAAAA GGGAGGAAAG 2340 TCACATTTAC TCTTAAGTAA ACCAGAGAAA GTTCTGTTGTTCCTTCCTGC CCATGGCTAT 2400 GGGGTGTCCA GTGGATAGGG ATGGCGGTGG GGAAAAGGAGAATACACTGG CCATTTATCC 2460 TGGACAAGCT CTTCCAGTCT GATGGAGGAG GTTCATGCCCTAGCCTAGAA AGGCCCAGGT 2520 CCATGACCCC CATCTTTGAG TTATGAGCAA GCTAAAAGAAGACACTATTT CTCACCATTT 2580 TGTGGAAATG GCCTGGGGAA CAAAGACTGA AATGGGCCTTGAGCCCACCT GCTACCTTGC 2640 AGAGAACCAT CTCGAGCCCC GTAGATCTTT TTAGGACCTCCACAGGCTAT TTCCCACCCC 2700 CCAGCCAAAA ATAGCTCAGA ATCTGCCCAT CCAGGGCTGTATTAATGATT TATGTAAAGG 2760 CAGATGGTTT ATTTCTACTT TGTAAAAGGG AAAAGTTGAGGTTCTGGAAG GATAAATGAT 2820 TTGCTCATGA GACAAAATCA AGGTTAGAAG TTACATGGAATTGTAGGACC AGAGCCATAT 2880 CATTAGATCA GCTTTCTGAA GAATATTCTC MAAAAAAGAAAGTCTCCTTG GCCAGATAAC 2940 TAAGAGGAAT GTTTCATTGT ATATCTTTTT TCTTGGAGATTTATATTAAC ATATTAAGTG 3000 CTCTGAGAAG TCCTGTGTAT TATCTCTTGC TGCATAATAAATTATCCCCA AACTTAAAAA 3060 AAAAAAAAAA AAAAAAACTC GAG 3083 235 aminoacids amino acid unknown protein unknown 37 Met Ser Arg Met Gly Lys ProIle Glu Thr Gln Lys Ser Pro Pro Pro 1 5 10 15 Pro Tyr Ser Arg Leu SerPro Arg Asp Glu Tyr Lys Pro Leu Asp Leu 20 25 30 Ser Asp Ser Thr Leu SerTyr Thr Glu Thr Glu Ala Thr Asn Ser Leu 35 40 45 Ile Thr Ala Pro Gly GluPhe Ser Asp Ala Ser Met Ser Pro Asp Ala 50 55 60 Thr Lys Pro Ser His TrpCys Ser Val Ala Tyr Trp Glu His Arg Thr 65 70 75 80 Arg Val Gly Arg LeuTyr Ala Val Tyr Asp Gln Ala Val Ser Ile Phe 85 90 95 Tyr Asp Leu Pro GlnGly Ser Gly Phe Cys Leu Gly Gln Leu Asn Leu 100 105 110 Glu Gln Arg SerGlu Ser Val Arg Arg Thr Arg Ser Lys Ile Gly Phe 115 120 125 Gly Ile LeuLeu Ser Lys Glu Pro Asp Gly Val Trp Ala Tyr Asn Arg 130 135 140 Gly GluHis Pro Ile Phe Val Asn Ser Pro Thr Leu Asp Ala Pro Gly 145 150 155 160Gly Arg Ala Leu Val Val Arg Lys Val Pro Pro Gly Tyr Ser Ile Lys 165 170175 Val Phe Asp Phe Glu Arg Ser Gly Leu Gln His Ala Pro Glu Pro Asp 180185 190 Ala Ala Asp Gly Pro Tyr Asp Pro Asn Ser Val Arg Ile Ser Phe Ala195 200 205 Lys Gly Trp Gly Pro Cys Tyr Ser Arg Gln Phe Ile Thr Ser CysPro 210 215 220 Cys Trp Leu Glu Ile Leu Leu Asn Asn Pro Arg 225 230 235375 amino acids amino acid unknown protein unknown 38 Met Asp Val ThrSer Gln Ala Arg Gly Val Gly Leu Glu Met Tyr Pro 1 5 10 15 Gly Thr AlaGln Pro Ala Ala Pro Asn Thr Thr Ser Pro Glu Leu Asn 20 25 30 Leu Ser HisPro Leu Leu Gly Thr Ala Leu Ala Asn Gly Thr Gly Glu 35 40 45 Leu Ser GluHis Gln Gln Tyr Val Ile Gly Leu Phe Leu Ser Cys Leu 50 55 60 Tyr Thr IlePhe Leu Phe Pro Ile Gly Phe Val Gly Asn Ile Leu Ile 65 70 75 80 Leu ValVal Asn Ile Ser Phe Arg Glu Lys Met Thr Ile Pro Asp Leu 85 90 95 Tyr PheIle Asn Leu Ala Val Ala Asp Leu Ile Leu Val Ala Asp Ser 100 105 110 LeuIle Glu Val Phe Asn Leu His Glu Arg Tyr Tyr Asp Ile Ala Val 115 120 125Leu Cys Thr Phe Met Ser Leu Phe Leu Arg Val Asn Met Tyr Ser Ser 130 135140 Val Phe Phe Leu Thr Trp Met Ser Phe Asp Arg Tyr Ile Ala Leu Ala 145150 155 160 Arg Ala Met Arg Cys Ser Leu Phe Arg Thr Lys His His Ala ArgLeu 165 170 175 Ser Cys Gly Leu Ile Trp Met Ala Ser Val Ser Ala Thr LeuVal Pro 180 185 190 Phe Thr Ala Val His Leu Gln His Thr Asp Glu Ala CysPhe Cys Phe 195 200 205 Ala Asp Val Arg Glu Val Gln Trp Leu Glu Val ThrLeu Gly Phe Ile 210 215 220 Val Pro Phe Ala Ile Ile Gly Leu Cys Tyr SerLeu Ile Val Arg Val 225 230 235 240 Leu Val Arg Ala His Arg His Arg GlyLeu Arg Pro Arg Arg Gln Lys 245 250 255 Ala Leu Arg Met Ile Leu Ala ValVal Leu Val Phe Phe Val Cys Trp 260 265 270 Leu Pro Glu Asn Val Phe IleSer Val His Leu Leu Gln Arg Thr Gln 275 280 285 Pro Gly Ala Ala Pro CysLys Gln Ser Phe Arg His Ala His Pro Leu 290 295 300 Thr Gly His Ile ValAsn Leu Ala Ala Phe Ser Asn Ser Cys Leu Asn 305 310 315 320 Pro Leu IleTyr Ser Phe Leu Gly Glu Thr Phe Arg Asp Lys Leu Arg 325 330 335 Leu TyrIle Glu Gln Lys Thr Asn Leu Pro Ala Leu Asp Arg Phe Cys 340 345 350 HisAla Ala Leu Lys Ala Val Ile Pro Asp Ser Thr Glu Gln Ser Asp 355 360 365Val Arg Phe Ser Ser Ala Val 370 375

What is claimed is:
 1. An isolated polynucleotide consisting of anucleotide sequence (a) encoding the amino acid sequence set forth inSEQ ID NO:37; or (b) encoding a polypeptide encoded by the cDNAcontained in plasmid pFCHD534, as deposited with the AgriculturalResearch Service Culture Collection as Accession Number B-21459.
 2. Anisolated polynucleotide consisting of the nucleotide sequence set forthin SEQ ID NO:36.
 3. An isolated polynucleotide consisting of thenucleotide sequence (a) set forth from nucleotide residue number 1032 to1736 of SEQ ID NO:36; or (b) of the polypeptide coding region of thecDNA contained in plasmid pFCHD534, as deposited with the AgriculturalResearch Service Culture Collection as Accession Number B-21459.
 4. Anisolated polynucleotide which hybridizes under highly stringentconditions to the polynucleotide of claim 1, wherein said polynucleotideencodes a polypeptide having 235 amino acids, said highly stringenthybridization conditions consisting of hybridization to filter-bound DNAin 0.5 M NaHPO₄, 7% sodium dodecyl sulfate, 1 mM EDTA at 65° C. andwashing in 0.1xSSC/0.1% SDS at 68° C., and wherein said polynucleotideis up-regulated in endothelial cells under conditions of increased shearstress.
 5. An isolated polynucleotide that hybridizes under highlystringent conditions to the polynucleotide of claim 3, wherein saidpolynucleotide encodes a polypeptide having 235 amino acids, said highlystringent hybridization conditions consisting of hybridization tofilter-bound DNA in 0.5 M NaBPO₄, 7% sodium dodecyl sulfate, 1 mM EDTAat 65° C. and washing in 0.1xSSC/0.1% SDS at 68° C., and wherein saidpolynucleotide is up-regulated in endothelial cells under conditions ofincreased shear stress.
 6. An isolated polynucleotide that hybridizesunder moderately stringent conditions to the polynucleotide of claim 3,wherein said polynucleotide encodes a polypeptide having 235 aminoacids, said moderately stringent hybridization conditions consisting ofhybridization to filter-bound DNA in 0.5 M NaHPO₄, 7% sodium dodecylsulfate, 1 mM EDTA at 65° C. and washing in 0.2xSSC/0.1% SDS at 42° C.;and wherein said polynucleotide is up-regulated in endothelial cellsunder conditions of increased shear stress.
 7. The isolatedpolynucleotide of claim 4, 5, 6, 1, 2, or 3, which is DNA.
 8. Theisolated polynucleotide of claim 7 which is cDNA.
 9. The isolatedpolynucleotide of claim 4, 5, 6, 1, 2, or 3, which is RNA.
 10. Theisolated polynucleotide of claim 4, 5, 6, 1, 2, or 3, which furthercomprises a label.
 11. A polynucleotide vector containing thepolynucleotide of claim 4, 5, 6, 1, 2, or
 3. 12. A polynucleotideexpression vector containing the polynucleotide of claim 4, 5, 6, 1, 2,or 3, in operative association with a nucleotide regulatory elementwhich controls expression of the polynucleotide in a host cell.
 13. Acultured genetically engineered host cell containing the polynucleotideof claim 4, 5, 6, 1, 2, or
 3. 14. A cultured genetically engineered hostcell containing the polynucleotide of claim 4, 5, 6, 1, 2, or 3, inoperative association with a nucleotide regulatory element whichcontrols expression of the polynucleotide in the host cell.
 15. Thegenetically engineered host cell of claim 14 which is prokaryotic. 16.The genetically engineered host cell of claim 14 which is eukaryotic.17. A method of producing an rchd534 polypeptide, comprising the stepsof: (a) growing the genetically engineered host cell of claim 15 in aculture; and (b) collecting the polypeptide gene product from theculture.
 18. A method of producing an rchd534 polypeptide, comprisingthe steps of: (a) growing the genetically engineered host cell of claim16 in a culture; and (b) collecting the polypeptide gene product fromthe culture.
 19. An isolated polynucleotide that hybridizes under highlystringent conditions to the polynucleotide of claim 1, said highlystringent hybridization conditions consisting of hybridization tofilter-bound DNA in 0.5 M NaHPO₄, 7% sodium dodecyl sulfate, 1 mM EDTAat 65° C. and washing in 0.1xSSC/0.1% SDS at 68° C., wherein saidisolated polynucleotide is up-regulated in endothelial cells underconditions of increased shear stress.
 20. An isolated polynucleotidethat hybridizes under highly stringent conditions to the polynucleotideof claim 3, said highly stringent hybridization conditions consisting ofhybridization to filter-bound DNA in 0.5 M NaHPO₄, 7% sodium dodecylsulfate, 1 mM EDTA at 65° C. and washing in 0.1xSSC/0.1% SDS at 68° C.and wherein said isolated polynucleotide is up-regulated in endothelialcells under conditions of increased shear stress.
 21. The isolatedpolynucleotide of claims 19 or 20 which is DNA.
 22. The isolatedpolynucleotide of claim 21 which is cDNA.
 23. The isolatedpolynucleotide of claims 19 or 20 which is RNA.
 24. The isolatedpolynucleotide of claims 19 or 20 which further comprises a label.
 25. Apolynucleotide vector containing the polynucleotide of claims 19 or 20.26. A polynucleotide expression vector containing the polynucleotide ofclaim 19 or 20 in operative association with a nucleotide regulatoryelement which controls expression of the polynucleotide in a host cell.27. A cultured genetically engineered host cell containing thepolynucleotide of claim 19 or
 20. 28. A cultured genetically engineeredhost cell containing the polynucleotide of claim 19 or 20 in operativeassociation with a nucleotide regulatory element which controlsexpression of the polynucleotide in the host cell.
 29. The geneticallyengineered host cell of claim 28 which is prokaryotic.
 30. Thegenetically engineered host cell of claim 28 which is eukaryotic.